Starting phenix.real_space_refine on Thu Sep 18 08:06:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zgl_11210/09_2025/6zgl_11210.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zgl_11210/09_2025/6zgl_11210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zgl_11210/09_2025/6zgl_11210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zgl_11210/09_2025/6zgl_11210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zgl_11210/09_2025/6zgl_11210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zgl_11210/09_2025/6zgl_11210.map" } resolution = 1.9 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 9324 2.51 5 N 2568 2.21 5 O 3832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15760 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 154, 1221 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} bond proxies already assigned to first conformer: 1225 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "J" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "K" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "L" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 2.11, per 1000 atoms: 0.13 Number of scatterers: 15760 At special positions: 0 Unit cell: (105.298, 101.422, 94.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3832 8.00 N 2568 7.00 C 9324 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: 1.32 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 238.4 nanoseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 22 through 54 Processing helix chain 'A' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 165 Processing helix chain 'B' and resid 22 through 54 Processing helix chain 'B' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 67 " --> pdb=" O HIS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 Processing helix chain 'C' and resid 22 through 54 Processing helix chain 'C' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 67 " --> pdb=" O HIS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 165 Processing helix chain 'D' and resid 22 through 54 Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 67 " --> pdb=" O HIS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 113 through 139 removed outlier: 4.272A pdb=" N GLY D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 165 Processing helix chain 'E' and resid 22 through 54 Processing helix chain 'E' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 67 " --> pdb=" O HIS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 102 Processing helix chain 'E' and resid 113 through 139 removed outlier: 4.272A pdb=" N GLY E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 165 Processing helix chain 'F' and resid 22 through 54 Processing helix chain 'F' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP F 67 " --> pdb=" O HIS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 102 Processing helix chain 'F' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 165 Processing helix chain 'G' and resid 22 through 54 Processing helix chain 'G' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP G 67 " --> pdb=" O HIS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 102 Processing helix chain 'G' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 165 Processing helix chain 'H' and resid 22 through 54 Processing helix chain 'H' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL H 62 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP H 67 " --> pdb=" O HIS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 102 Processing helix chain 'H' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY H 137 " --> pdb=" O ARG H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 165 Processing helix chain 'I' and resid 22 through 54 Processing helix chain 'I' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL I 62 " --> pdb=" O ASN I 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP I 67 " --> pdb=" O HIS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'I' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY I 137 " --> pdb=" O ARG I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 165 Processing helix chain 'J' and resid 22 through 54 Processing helix chain 'J' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL J 62 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP J 67 " --> pdb=" O HIS J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 102 Processing helix chain 'J' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 165 Processing helix chain 'K' and resid 22 through 54 Processing helix chain 'K' and resid 58 through 87 removed outlier: 3.575A pdb=" N VAL K 62 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP K 67 " --> pdb=" O HIS K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 102 Processing helix chain 'K' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY K 137 " --> pdb=" O ARG K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 165 Processing helix chain 'L' and resid 22 through 54 Processing helix chain 'L' and resid 58 through 87 removed outlier: 3.574A pdb=" N VAL L 62 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP L 67 " --> pdb=" O HIS L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 102 Processing helix chain 'L' and resid 113 through 139 removed outlier: 4.273A pdb=" N GLY L 137 " --> pdb=" O ARG L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 165 1212 hydrogen bonds defined for protein. 3612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 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: 1.20 - 1.33: 3925 1.33 - 1.46: 3738 1.46 - 1.59: 7301 1.59 - 1.72: 0 1.72 - 1.85: 72 Bond restraints: 15036 Sorted by residual: bond pdb=" C GLU G 31 " pdb=" CA BGLU G 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.76e+01 bond pdb=" C GLU E 31 " pdb=" CA BGLU E 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.75e+01 bond pdb=" C GLU J 31 " pdb=" CA BGLU J 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.75e+01 bond pdb=" C GLU I 31 " pdb=" CA BGLU I 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.74e+01 bond pdb=" C GLU F 31 " pdb=" CA BGLU F 31 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.74e+01 ... (remaining 15031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 15613 1.68 - 3.35: 3938 3.35 - 5.03: 669 5.03 - 6.70: 156 6.70 - 8.38: 24 Bond angle restraints: 20400 Sorted by residual: angle pdb=" CA SER D 100 " pdb=" C SER D 100 " pdb=" O SER D 100 " ideal model delta sigma weight residual 119.79 128.17 -8.38 1.18e+00 7.18e-01 5.04e+01 angle pdb=" CA SER E 100 " pdb=" C SER E 100 " pdb=" O SER E 100 " ideal model delta sigma weight residual 119.79 128.14 -8.35 1.18e+00 7.18e-01 5.01e+01 angle pdb=" CA SER J 100 " pdb=" C SER J 100 " pdb=" O SER J 100 " ideal model delta sigma weight residual 119.79 128.13 -8.34 1.18e+00 7.18e-01 4.99e+01 angle pdb=" CA SER H 100 " pdb=" C SER H 100 " pdb=" O SER H 100 " ideal model delta sigma weight residual 119.79 128.13 -8.34 1.18e+00 7.18e-01 4.99e+01 angle pdb=" CA SER F 100 " pdb=" C SER F 100 " pdb=" O SER F 100 " ideal model delta sigma weight residual 119.79 128.13 -8.34 1.18e+00 7.18e-01 4.99e+01 ... (remaining 20395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 7995 17.43 - 34.87: 981 34.87 - 52.30: 144 52.30 - 69.74: 60 69.74 - 87.17: 12 Dihedral angle restraints: 9192 sinusoidal: 3672 harmonic: 5520 Sorted by residual: dihedral pdb=" C THR B 29 " pdb=" N THR B 29 " pdb=" CA THR B 29 " pdb=" CB THR B 29 " ideal model delta harmonic sigma weight residual -122.00 -131.91 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C THR E 29 " pdb=" N THR E 29 " pdb=" CA THR E 29 " pdb=" CB THR E 29 " ideal model delta harmonic sigma weight residual -122.00 -131.90 9.90 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C THR D 29 " pdb=" N THR D 29 " pdb=" CA THR D 29 " pdb=" CB THR D 29 " ideal model delta harmonic sigma weight residual -122.00 -131.90 9.90 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 9189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1762 0.107 - 0.213: 519 0.213 - 0.319: 71 0.319 - 0.426: 28 0.426 - 0.532: 20 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CG LEU D 66 " pdb=" CB LEU D 66 " pdb=" CD1 LEU D 66 " pdb=" CD2 LEU D 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CG LEU B 66 " pdb=" CB LEU B 66 " pdb=" CD1 LEU B 66 " pdb=" CD2 LEU B 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CG LEU K 66 " pdb=" CB LEU K 66 " pdb=" CD1 LEU K 66 " pdb=" CD2 LEU K 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.08e+00 ... (remaining 2397 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 59 " 0.018 2.00e-02 2.50e+03 4.43e-02 3.43e+01 pdb=" CG PHE F 59 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE F 59 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE F 59 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE F 59 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE F 59 " 0.081 2.00e-02 2.50e+03 pdb=" CZ PHE F 59 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 59 " 0.018 2.00e-02 2.50e+03 4.42e-02 3.42e+01 pdb=" CG PHE K 59 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE K 59 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE K 59 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE K 59 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE K 59 " 0.081 2.00e-02 2.50e+03 pdb=" CZ PHE K 59 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 59 " -0.018 2.00e-02 2.50e+03 4.42e-02 3.42e+01 pdb=" CG PHE B 59 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 59 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 59 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE B 59 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE B 59 " -0.081 2.00e-02 2.50e+03 pdb=" CZ PHE B 59 " 0.056 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1998 2.74 - 3.28: 18358 3.28 - 3.82: 31261 3.82 - 4.36: 38557 4.36 - 4.90: 62168 Nonbonded interactions: 152342 Sorted by model distance: nonbonded pdb=" OD1 ASP E 75 " pdb=" O HOH E 201 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASP I 75 " pdb=" O HOH I 201 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP H 75 " pdb=" O HOH H 201 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP J 75 " pdb=" O HOH J 201 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP L 75 " pdb=" O HOH L 201 " model vdw 2.204 3.040 ... (remaining 152337 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.013 0.067 15036 Z= 0.801 Angle : 1.549 8.379 20400 Z= 1.068 Chirality : 0.115 0.532 2400 Planarity : 0.010 0.044 2640 Dihedral : 15.524 87.169 5592 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.73 % Allowed : 8.21 % Favored : 88.06 % 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: 0.13 (0.17), residues: 1848 helix: 0.45 (0.12), residues: 1404 sheet: None (None), residues: 0 loop : -0.77 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.005 ARG L 124 TYR 0.036 0.014 TYR J 16 PHE 0.081 0.012 PHE F 59 TRP 0.027 0.013 TRP I 160 HIS 0.010 0.003 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.01294 (15036) covalent geometry : angle 1.54903 (20400) hydrogen bonds : bond 0.21630 ( 1212) hydrogen bonds : angle 6.13417 ( 3612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.550 Fit side-chains REVERT: A 25 GLU cc_start: 0.6760 (tt0) cc_final: 0.6329 (tp30) REVERT: A 134 LYS cc_start: 0.7747 (mttp) cc_final: 0.7534 (mttt) REVERT: B 25 GLU cc_start: 0.6780 (tt0) cc_final: 0.6328 (tp30) REVERT: B 142 ASP cc_start: 0.7973 (m-30) cc_final: 0.7734 (m-30) REVERT: C 25 GLU cc_start: 0.6764 (tt0) cc_final: 0.6331 (tp30) REVERT: C 101 LYS cc_start: 0.7221 (mttt) cc_final: 0.6932 (mttm) REVERT: D 101 LYS cc_start: 0.7262 (mttt) cc_final: 0.7023 (mttm) REVERT: D 134 LYS cc_start: 0.7748 (mttp) cc_final: 0.7537 (mttp) REVERT: D 138 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: E 22 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7557 (p) REVERT: E 25 GLU cc_start: 0.6758 (tt0) cc_final: 0.6317 (tp30) REVERT: E 134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7486 (mttp) REVERT: F 25 GLU cc_start: 0.6737 (tt0) cc_final: 0.6352 (tp30) REVERT: F 70 ARG cc_start: 0.8416 (ttt180) cc_final: 0.7465 (ttp80) REVERT: F 75 ASP cc_start: 0.8570 (m-30) cc_final: 0.8297 (t70) REVERT: F 101 LYS cc_start: 0.7181 (mttt) cc_final: 0.6896 (mttm) REVERT: F 134 LYS cc_start: 0.7664 (mttp) cc_final: 0.7463 (mttt) REVERT: G 25 GLU cc_start: 0.6671 (tt0) cc_final: 0.6261 (tp30) REVERT: G 35 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7730 (mtm110) REVERT: G 134 LYS cc_start: 0.7695 (mttp) cc_final: 0.7478 (mttm) REVERT: H 24 SER cc_start: 0.7174 (OUTLIER) cc_final: 0.6967 (p) REVERT: H 25 GLU cc_start: 0.6767 (tt0) cc_final: 0.6349 (tp30) REVERT: H 70 ARG cc_start: 0.8426 (ttt180) cc_final: 0.8116 (ttt180) REVERT: H 75 ASP cc_start: 0.8558 (m-30) cc_final: 0.8269 (t70) REVERT: H 120 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8180 (mm-30) REVERT: H 138 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: H 142 ASP cc_start: 0.7942 (m-30) cc_final: 0.7644 (m-30) REVERT: I 25 GLU cc_start: 0.6744 (tt0) cc_final: 0.6359 (tp30) REVERT: I 101 LYS cc_start: 0.7180 (mttt) cc_final: 0.6910 (mttm) REVERT: J 35 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7695 (mtm110) REVERT: J 101 LYS cc_start: 0.7248 (mttt) cc_final: 0.7033 (mttm) REVERT: J 134 LYS cc_start: 0.7731 (mttp) cc_final: 0.7489 (mttp) REVERT: J 142 ASP cc_start: 0.8001 (m-30) cc_final: 0.7790 (m-30) REVERT: K 25 GLU cc_start: 0.6860 (tt0) cc_final: 0.6367 (tp30) REVERT: K 134 LYS cc_start: 0.7733 (mttp) cc_final: 0.7154 (mtpt) REVERT: K 142 ASP cc_start: 0.8026 (m-30) cc_final: 0.7781 (m-30) REVERT: L 25 GLU cc_start: 0.6769 (tt0) cc_final: 0.6321 (tp30) REVERT: L 101 LYS cc_start: 0.7307 (mttt) cc_final: 0.7052 (mttm) REVERT: L 142 ASP cc_start: 0.7957 (m-30) cc_final: 0.7726 (m-30) outliers start: 48 outliers final: 9 residues processed: 287 average time/residue: 0.9437 time to fit residues: 289.2069 Evaluate side-chains 288 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 35 ARG Chi-restraints excluded: chain L residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN D 113 ASN E 113 ASN F 113 ASN G 113 ASN I 113 ASN J 99 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.171717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.157644 restraints weight = 45042.576| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.07 r_work: 0.3572 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15036 Z= 0.187 Angle : 0.618 7.280 20400 Z= 0.352 Chirality : 0.043 0.147 2400 Planarity : 0.004 0.027 2640 Dihedral : 4.838 36.654 2053 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.06 % Allowed : 9.14 % Favored : 89.80 % 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: 2.99 (0.17), residues: 1848 helix: 2.45 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.29 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 153 TYR 0.010 0.002 TYR C 16 PHE 0.012 0.002 PHE C 59 TRP 0.004 0.001 TRP E 160 HIS 0.007 0.002 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00336 (15036) covalent geometry : angle 0.61778 (20400) hydrogen bonds : bond 0.08758 ( 1212) hydrogen bonds : angle 4.17661 ( 3612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 283 time to evaluate : 0.543 Fit side-chains REVERT: A 134 LYS cc_start: 0.7843 (mttp) cc_final: 0.7635 (mttp) REVERT: E 134 LYS cc_start: 0.7901 (mttp) cc_final: 0.7658 (mttp) REVERT: F 55 ARG cc_start: 0.8000 (ptp90) cc_final: 0.7793 (ptm160) REVERT: F 70 ARG cc_start: 0.8320 (ttt180) cc_final: 0.7592 (ttp80) REVERT: F 134 LYS cc_start: 0.7860 (mttp) cc_final: 0.7517 (mtpt) REVERT: G 134 LYS cc_start: 0.7921 (mttp) cc_final: 0.7688 (mttp) REVERT: H 35 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7749 (ttp80) REVERT: I 134 LYS cc_start: 0.7941 (mttp) cc_final: 0.7702 (mtpt) REVERT: J 101 LYS cc_start: 0.7570 (mttt) cc_final: 0.7291 (mttm) outliers start: 5 outliers final: 3 residues processed: 283 average time/residue: 0.9889 time to fit residues: 297.9704 Evaluate side-chains 267 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 264 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN D 39 GLN D 113 ASN E 39 GLN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 113 ASN J 39 GLN K 113 ASN L 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.169389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.155658 restraints weight = 39429.954| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 0.95 r_work: 0.3547 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15036 Z= 0.237 Angle : 0.693 7.801 20400 Z= 0.395 Chirality : 0.045 0.179 2400 Planarity : 0.005 0.048 2640 Dihedral : 4.412 19.225 2028 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.24 % Allowed : 9.76 % Favored : 88.99 % 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: 2.60 (0.17), residues: 1848 helix: 2.11 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.42 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 124 TYR 0.013 0.002 TYR C 16 PHE 0.015 0.003 PHE C 59 TRP 0.005 0.002 TRP A 160 HIS 0.008 0.003 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00464 (15036) covalent geometry : angle 0.69275 (20400) hydrogen bonds : bond 0.09639 ( 1212) hydrogen bonds : angle 4.34794 ( 3612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 276 time to evaluate : 0.677 Fit side-chains REVERT: A 55 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7635 (ptm160) REVERT: A 134 LYS cc_start: 0.7947 (mttp) cc_final: 0.7734 (mttp) REVERT: E 134 LYS cc_start: 0.7905 (mttp) cc_final: 0.7658 (mttp) REVERT: F 134 LYS cc_start: 0.7957 (mttp) cc_final: 0.7630 (mtpt) REVERT: G 134 LYS cc_start: 0.7929 (mttp) cc_final: 0.7719 (mttp) REVERT: I 134 LYS cc_start: 0.7999 (mttp) cc_final: 0.7727 (mtpt) REVERT: J 55 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7764 (ptm160) outliers start: 8 outliers final: 4 residues processed: 276 average time/residue: 1.0456 time to fit residues: 307.3233 Evaluate side-chains 278 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 272 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 176 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 113 ASN D 113 ASN E 39 GLN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.173819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.159651 restraints weight = 48682.866| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.15 r_work: 0.3605 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15036 Z= 0.166 Angle : 0.560 6.533 20400 Z= 0.316 Chirality : 0.040 0.129 2400 Planarity : 0.003 0.023 2640 Dihedral : 4.199 18.765 2028 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.06 % Allowed : 10.57 % Favored : 88.37 % 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: 3.30 (0.17), residues: 1848 helix: 2.57 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.77 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 35 TYR 0.008 0.001 TYR C 16 PHE 0.007 0.001 PHE L 69 TRP 0.004 0.001 TRP I 52 HIS 0.006 0.002 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00286 (15036) covalent geometry : angle 0.55982 (20400) hydrogen bonds : bond 0.08018 ( 1212) hydrogen bonds : angle 3.98948 ( 3612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 294 time to evaluate : 0.728 Fit side-chains REVERT: A 35 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7738 (ttp80) REVERT: A 134 LYS cc_start: 0.7851 (mttp) cc_final: 0.7618 (mttp) REVERT: B 35 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7597 (ttp80) REVERT: F 55 ARG cc_start: 0.8033 (ptp90) cc_final: 0.7801 (ptm160) REVERT: F 134 LYS cc_start: 0.7855 (mttp) cc_final: 0.7492 (mtpt) REVERT: H 140 LYS cc_start: 0.7028 (mmtt) cc_final: 0.6673 (mtmt) REVERT: I 134 LYS cc_start: 0.7931 (mttp) cc_final: 0.7663 (mtpt) outliers start: 5 outliers final: 4 residues processed: 294 average time/residue: 1.0100 time to fit residues: 316.3571 Evaluate side-chains 290 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 286 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 39 GLN C 113 ASN E 39 GLN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 113 ASN L 113 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.170034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.156290 restraints weight = 40842.515| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 0.93 r_work: 0.3567 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15036 Z= 0.235 Angle : 0.679 9.632 20400 Z= 0.387 Chirality : 0.045 0.168 2400 Planarity : 0.005 0.046 2640 Dihedral : 4.437 19.406 2028 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.31 % Allowed : 10.63 % Favored : 88.06 % 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: 2.72 (0.17), residues: 1848 helix: 2.18 (0.12), residues: 1440 sheet: None (None), residues: 0 loop : 0.52 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 124 TYR 0.013 0.002 TYR C 16 PHE 0.013 0.003 PHE C 59 TRP 0.005 0.002 TRP A 160 HIS 0.009 0.003 HIS K 63 Details of bonding type rmsd covalent geometry : bond 0.00461 (15036) covalent geometry : angle 0.67907 (20400) hydrogen bonds : bond 0.09519 ( 1212) hydrogen bonds : angle 4.30381 ( 3612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 289 time to evaluate : 0.559 Fit side-chains REVERT: A 55 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7561 (ptm160) REVERT: A 134 LYS cc_start: 0.7908 (mttp) cc_final: 0.7676 (mttp) REVERT: A 142 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: F 134 LYS cc_start: 0.7916 (mttp) cc_final: 0.7590 (mtpt) REVERT: H 120 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8264 (mm-30) REVERT: I 134 LYS cc_start: 0.7939 (mttp) cc_final: 0.7686 (mtpt) REVERT: J 55 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7721 (ptm160) outliers start: 9 outliers final: 3 residues processed: 289 average time/residue: 1.0142 time to fit residues: 312.5412 Evaluate side-chains 288 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 282 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 113 ASN B 113 ASN C 39 GLN C 113 ASN D 113 ASN E 39 GLN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.175171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.161635 restraints weight = 40247.484| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 0.96 r_work: 0.3624 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15036 Z= 0.159 Angle : 0.543 8.180 20400 Z= 0.305 Chirality : 0.039 0.120 2400 Planarity : 0.003 0.020 2640 Dihedral : 4.172 18.707 2028 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.24 % Allowed : 10.63 % Favored : 88.12 % 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: 3.36 (0.18), residues: 1848 helix: 2.61 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.74 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 55 TYR 0.007 0.001 TYR C 16 PHE 0.006 0.001 PHE L 69 TRP 0.004 0.001 TRP I 52 HIS 0.006 0.002 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00271 (15036) covalent geometry : angle 0.54313 (20400) hydrogen bonds : bond 0.07721 ( 1212) hydrogen bonds : angle 3.92775 ( 3612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 293 time to evaluate : 0.664 Fit side-chains REVERT: A 35 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7709 (ttp80) REVERT: A 134 LYS cc_start: 0.7827 (mttp) cc_final: 0.7576 (mttt) REVERT: A 138 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6452 (mp0) REVERT: B 35 ARG cc_start: 0.7845 (mtp-110) cc_final: 0.7613 (ttp80) REVERT: B 70 ARG cc_start: 0.8386 (tpt170) cc_final: 0.8016 (ttt-90) REVERT: F 55 ARG cc_start: 0.8024 (ptp90) cc_final: 0.7781 (ptm160) REVERT: F 134 LYS cc_start: 0.7856 (mttp) cc_final: 0.7505 (mtpt) REVERT: G 35 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7769 (ttp80) REVERT: I 134 LYS cc_start: 0.7889 (mttp) cc_final: 0.7512 (mtpt) REVERT: I 138 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: J 55 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7463 (ptm160) REVERT: J 101 LYS cc_start: 0.7539 (mttp) cc_final: 0.7295 (mttm) REVERT: K 138 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6356 (mp0) outliers start: 8 outliers final: 3 residues processed: 293 average time/residue: 1.0223 time to fit residues: 319.1008 Evaluate side-chains 287 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.0030 chunk 107 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 39 GLN C 113 ASN E 113 ASN F 113 ASN G 113 ASN I 39 GLN I 113 ASN J 39 GLN L 113 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.178748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.164968 restraints weight = 49140.918| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.15 r_work: 0.3668 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15036 Z= 0.145 Angle : 0.507 7.615 20400 Z= 0.283 Chirality : 0.038 0.110 2400 Planarity : 0.003 0.018 2640 Dihedral : 4.013 18.307 2028 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.18 % Allowed : 11.26 % Favored : 87.56 % 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: 3.70 (0.18), residues: 1848 helix: 2.86 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.81 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 55 TYR 0.006 0.001 TYR K 16 PHE 0.007 0.001 PHE H 69 TRP 0.004 0.001 TRP I 52 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00239 (15036) covalent geometry : angle 0.50676 (20400) hydrogen bonds : bond 0.07090 ( 1212) hydrogen bonds : angle 3.78747 ( 3612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 303 time to evaluate : 0.666 Fit side-chains REVERT: A 35 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7685 (ttp80) REVERT: A 70 ARG cc_start: 0.8289 (tpt170) cc_final: 0.7888 (ttt-90) REVERT: A 134 LYS cc_start: 0.7783 (mttp) cc_final: 0.7392 (mtpt) REVERT: A 138 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: B 70 ARG cc_start: 0.8388 (tpt170) cc_final: 0.8036 (ttt-90) REVERT: B 140 LYS cc_start: 0.7216 (mmtt) cc_final: 0.6851 (mtmt) REVERT: C 70 ARG cc_start: 0.8298 (ttt180) cc_final: 0.7670 (ttp80) REVERT: F 70 ARG cc_start: 0.8301 (ttt180) cc_final: 0.7592 (ttp80) REVERT: F 134 LYS cc_start: 0.7856 (mttp) cc_final: 0.7512 (mtpt) REVERT: G 35 ARG cc_start: 0.7884 (mtp-110) cc_final: 0.7644 (ttp80) REVERT: H 35 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7629 (ttp80) REVERT: I 134 LYS cc_start: 0.7773 (mttp) cc_final: 0.7450 (mtpt) REVERT: I 138 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: J 35 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7680 (ttp80) REVERT: K 70 ARG cc_start: 0.8314 (ttt180) cc_final: 0.7700 (ttp80) REVERT: K 138 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6325 (mp0) REVERT: L 35 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7663 (ttp80) outliers start: 7 outliers final: 2 residues processed: 303 average time/residue: 1.0201 time to fit residues: 329.2894 Evaluate side-chains 290 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 286 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.171012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.156595 restraints weight = 47995.797| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.16 r_work: 0.3561 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15036 Z= 0.220 Angle : 0.651 8.463 20400 Z= 0.370 Chirality : 0.044 0.168 2400 Planarity : 0.005 0.053 2640 Dihedral : 4.345 19.458 2028 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.18 % Allowed : 11.26 % Favored : 87.56 % 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: 3.03 (0.17), residues: 1848 helix: 2.35 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.82 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 55 TYR 0.012 0.002 TYR C 16 PHE 0.013 0.003 PHE C 59 TRP 0.004 0.002 TRP A 160 HIS 0.008 0.003 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00425 (15036) covalent geometry : angle 0.65149 (20400) hydrogen bonds : bond 0.09193 ( 1212) hydrogen bonds : angle 4.21062 ( 3612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 287 time to evaluate : 0.652 Fit side-chains REVERT: A 55 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7436 (ptm160) REVERT: A 134 LYS cc_start: 0.7903 (mttp) cc_final: 0.7694 (mttt) REVERT: F 134 LYS cc_start: 0.7939 (mttp) cc_final: 0.7584 (mtpt) REVERT: H 120 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8267 (mm-30) REVERT: I 134 LYS cc_start: 0.7988 (mttp) cc_final: 0.7723 (mtpt) REVERT: J 55 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7550 (ptm160) REVERT: J 101 LYS cc_start: 0.7552 (mttp) cc_final: 0.7304 (mttm) outliers start: 7 outliers final: 2 residues processed: 287 average time/residue: 1.0335 time to fit residues: 315.8303 Evaluate side-chains 285 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 281 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 174 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN C 113 ASN D 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN K 113 ASN L 113 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.174863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.161363 restraints weight = 41104.691| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.01 r_work: 0.3625 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15036 Z= 0.161 Angle : 0.548 8.014 20400 Z= 0.307 Chirality : 0.039 0.120 2400 Planarity : 0.003 0.027 2640 Dihedral : 4.160 18.799 2028 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.00 % Allowed : 11.32 % Favored : 87.69 % 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: 3.52 (0.18), residues: 1848 helix: 2.72 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.88 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 18 TYR 0.008 0.001 TYR C 16 PHE 0.005 0.001 PHE L 69 TRP 0.004 0.001 TRP I 52 HIS 0.006 0.002 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00276 (15036) covalent geometry : angle 0.54770 (20400) hydrogen bonds : bond 0.07774 ( 1212) hydrogen bonds : angle 3.92788 ( 3612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 290 time to evaluate : 0.443 Fit side-chains REVERT: A 134 LYS cc_start: 0.7836 (mttp) cc_final: 0.7554 (mtpt) REVERT: B 70 ARG cc_start: 0.8372 (tpt170) cc_final: 0.8003 (ttt-90) REVERT: B 140 LYS cc_start: 0.7276 (mmtt) cc_final: 0.6945 (mtmt) REVERT: C 70 ARG cc_start: 0.8330 (ttt180) cc_final: 0.7685 (ttp80) REVERT: F 134 LYS cc_start: 0.7867 (mttp) cc_final: 0.7510 (mtpt) REVERT: I 134 LYS cc_start: 0.7898 (mttp) cc_final: 0.7667 (mtpt) REVERT: J 35 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7782 (ttp80) REVERT: J 55 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7422 (ptm160) REVERT: J 101 LYS cc_start: 0.7518 (mttp) cc_final: 0.7267 (mttm) REVERT: K 138 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6390 (mp0) outliers start: 4 outliers final: 3 residues processed: 291 average time/residue: 1.0028 time to fit residues: 311.0108 Evaluate side-chains 291 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 287 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain K residue 17 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN C 39 GLN C 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN L 113 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.177640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.163918 restraints weight = 46916.813| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.16 r_work: 0.3646 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15036 Z= 0.149 Angle : 0.520 7.909 20400 Z= 0.290 Chirality : 0.038 0.111 2400 Planarity : 0.003 0.022 2640 Dihedral : 4.049 18.342 2028 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.87 % Allowed : 11.57 % Favored : 87.56 % 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: 3.70 (0.18), residues: 1848 helix: 2.86 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : 0.81 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 18 TYR 0.006 0.001 TYR C 16 PHE 0.008 0.001 PHE H 69 TRP 0.004 0.001 TRP I 52 HIS 0.005 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00249 (15036) covalent geometry : angle 0.52027 (20400) hydrogen bonds : bond 0.07286 ( 1212) hydrogen bonds : angle 3.82688 ( 3612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 0.630 Fit side-chains REVERT: A 70 ARG cc_start: 0.8315 (tpt170) cc_final: 0.7901 (ttt-90) REVERT: A 134 LYS cc_start: 0.7778 (mttp) cc_final: 0.7471 (mtpt) REVERT: B 70 ARG cc_start: 0.8401 (tpt170) cc_final: 0.8042 (ttt-90) REVERT: B 140 LYS cc_start: 0.7218 (mmtt) cc_final: 0.6876 (mtmt) REVERT: C 70 ARG cc_start: 0.8345 (ttt180) cc_final: 0.7695 (ttp80) REVERT: F 134 LYS cc_start: 0.7868 (mttp) cc_final: 0.7507 (mtpt) REVERT: G 35 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7649 (ttp80) REVERT: H 35 ARG cc_start: 0.7861 (mtp-110) cc_final: 0.7648 (ttp80) REVERT: J 55 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7421 (ptm160) REVERT: J 70 ARG cc_start: 0.8303 (ttt180) cc_final: 0.8041 (ttt-90) REVERT: J 101 LYS cc_start: 0.7493 (mttp) cc_final: 0.7244 (mttm) REVERT: K 138 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6338 (mp0) outliers start: 2 outliers final: 1 residues processed: 287 average time/residue: 0.9889 time to fit residues: 302.7971 Evaluate side-chains 283 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain J residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 104 optimal weight: 0.0030 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN C 113 ASN D 39 GLN D 113 ASN E 113 ASN F 113 ASN G 113 ASN H 113 ASN I 39 GLN I 113 ASN J 39 GLN K 113 ASN L 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.172138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.158743 restraints weight = 37830.010| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 0.90 r_work: 0.3603 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15036 Z= 0.185 Angle : 0.594 9.292 20400 Z= 0.335 Chirality : 0.041 0.152 2400 Planarity : 0.004 0.038 2640 Dihedral : 4.206 19.247 2028 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.93 % Allowed : 11.50 % Favored : 87.56 % 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: 3.37 (0.18), residues: 1848 helix: 2.61 (0.12), residues: 1452 sheet: None (None), residues: 0 loop : 0.85 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 70 TYR 0.009 0.001 TYR F 16 PHE 0.008 0.002 PHE C 59 TRP 0.003 0.001 TRP K 52 HIS 0.008 0.002 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00336 (15036) covalent geometry : angle 0.59423 (20400) hydrogen bonds : bond 0.08487 ( 1212) hydrogen bonds : angle 4.05201 ( 3612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8686.40 seconds wall clock time: 148 minutes 24.07 seconds (8904.07 seconds total)