Starting phenix.real_space_refine on Tue Feb 3 15:28:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1o_62750/02_2026/9l1o_62750.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1o_62750/02_2026/9l1o_62750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l1o_62750/02_2026/9l1o_62750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1o_62750/02_2026/9l1o_62750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l1o_62750/02_2026/9l1o_62750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1o_62750/02_2026/9l1o_62750.map" } resolution = 3.7 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= 0.063 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 19 5.16 5 C 2678 2.51 5 N 714 2.21 5 O 842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4253 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 889 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1710 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "L" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Time building chain proxies: 1.11, per 1000 atoms: 0.26 Number of scatterers: 4253 At special positions: 0 Unit cell: (63.046, 117.396, 68.481, 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 19 16.00 O 842 8.00 N 714 7.00 C 2678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.10 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.09 Simple disulfide: pdb=" SG CYS H 225 " - pdb=" SG CYS L 214 " distance=1.99 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 166.3 milliseconds 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 14 sheets defined 5.6% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.901A pdb=" N ASN H 66 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.131A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 213 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'E' and resid 33 through 34 removed outlier: 3.683A pdb=" N ALA E 110 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.136A pdb=" N ILE E 40 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 85 removed outlier: 4.780A pdb=" N VAL E 78 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP E 67 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 78 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU E 65 " --> pdb=" O VAL E 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.502A pdb=" N ALA H 16 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL H 18 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N SER H 84 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU H 20 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLU H 82 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS H 22 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR H 80 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA H 24 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N THR H 78 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.345A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.941A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.346A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 154 " --> pdb=" O TYR H 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 161 through 163 Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.871A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.950A pdb=" N LYS L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.502A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.611A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.079A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 315 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: 0.53 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 923 1.32 - 1.45: 1270 1.45 - 1.59: 2111 1.59 - 1.72: 24 1.72 - 1.85: 21 Bond restraints: 4349 Sorted by residual: bond pdb=" CD2 HIS L 24 " pdb=" NE2 HIS L 24 " ideal model delta sigma weight residual 1.374 1.466 -0.092 1.10e-02 8.26e+03 7.05e+01 bond pdb=" ND1 HIS H 173 " pdb=" CE1 HIS H 173 " ideal model delta sigma weight residual 1.321 1.391 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" CD2 HIS L 198 " pdb=" NE2 HIS L 198 " ideal model delta sigma weight residual 1.374 1.450 -0.076 1.10e-02 8.26e+03 4.77e+01 bond pdb=" CD2 HIS H 173 " pdb=" NE2 HIS H 173 " ideal model delta sigma weight residual 1.374 1.448 -0.074 1.10e-02 8.26e+03 4.48e+01 bond pdb=" C PRO L 119 " pdb=" O PRO L 119 " ideal model delta sigma weight residual 1.246 1.190 0.055 8.50e-03 1.38e+04 4.25e+01 ... (remaining 4344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 3934 1.85 - 3.71: 1372 3.71 - 5.56: 501 5.56 - 7.42: 83 7.42 - 9.27: 15 Bond angle restraints: 5905 Sorted by residual: angle pdb=" O PRO L 119 " pdb=" C PRO L 119 " pdb=" N PRO L 120 " ideal model delta sigma weight residual 121.31 125.54 -4.23 4.60e-01 4.73e+00 8.45e+01 angle pdb=" CD2 HIS H 173 " pdb=" NE2 HIS H 173 " pdb=" CE1 HIS H 173 " ideal model delta sigma weight residual 109.00 100.82 8.18 1.00e+00 1.00e+00 6.70e+01 angle pdb=" CA PRO L 119 " pdb=" C PRO L 119 " pdb=" O PRO L 119 " ideal model delta sigma weight residual 120.90 115.67 5.23 7.20e-01 1.93e+00 5.27e+01 angle pdb=" N SER H 122 " pdb=" CA SER H 122 " pdb=" C SER H 122 " ideal model delta sigma weight residual 113.28 104.44 8.84 1.22e+00 6.72e-01 5.25e+01 angle pdb=" CD2 HIS L 24 " pdb=" NE2 HIS L 24 " pdb=" CE1 HIS L 24 " ideal model delta sigma weight residual 109.00 101.82 7.18 1.00e+00 1.00e+00 5.16e+01 ... (remaining 5900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 2419 17.83 - 35.65: 160 35.65 - 53.47: 23 53.47 - 71.30: 11 71.30 - 89.12: 9 Dihedral angle restraints: 2622 sinusoidal: 1015 harmonic: 1607 Sorted by residual: dihedral pdb=" CB CYS E 52 " pdb=" SG CYS E 52 " pdb=" SG CYS E 126 " pdb=" CB CYS E 126 " ideal model delta sinusoidal sigma weight residual 93.00 166.52 -73.52 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 35.67 57.33 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CA THR H 30 " pdb=" C THR H 30 " pdb=" N ARG H 31 " pdb=" CA ARG H 31 " ideal model delta harmonic sigma weight residual -180.00 -147.31 -32.69 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 2619 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.124: 356 0.124 - 0.247: 222 0.247 - 0.369: 64 0.369 - 0.492: 12 0.492 - 0.614: 6 Chirality restraints: 660 Sorted by residual: chirality pdb=" CG LEU L 175 " pdb=" CB LEU L 175 " pdb=" CD1 LEU L 175 " pdb=" CD2 LEU L 175 " both_signs ideal model delta sigma weight residual False -2.59 -3.20 0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" CG LEU H 20 " pdb=" CB LEU H 20 " pdb=" CD1 LEU H 20 " pdb=" CD2 LEU H 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.19e+00 chirality pdb=" CG LEU H 45 " pdb=" CB LEU H 45 " pdb=" CD1 LEU H 45 " pdb=" CD2 LEU H 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.86e+00 ... (remaining 657 not shown) Planarity restraints: 757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 163 " 0.112 2.00e-02 2.50e+03 9.56e-02 2.28e+02 pdb=" CG TRP H 163 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP H 163 " -0.169 2.00e-02 2.50e+03 pdb=" CD2 TRP H 163 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 163 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP H 163 " 0.056 2.00e-02 2.50e+03 pdb=" CE3 TRP H 163 " -0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 163 " 0.133 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 163 " -0.107 2.00e-02 2.50e+03 pdb=" CH2 TRP H 163 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 35 " -0.059 2.00e-02 2.50e+03 7.36e-02 1.35e+02 pdb=" CG TRP L 35 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP L 35 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP L 35 " 0.107 2.00e-02 2.50e+03 pdb=" NE1 TRP L 35 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP L 35 " 0.075 2.00e-02 2.50e+03 pdb=" CE3 TRP L 35 " 0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 35 " 0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 35 " -0.084 2.00e-02 2.50e+03 pdb=" CH2 TRP L 35 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.023 2.00e-02 2.50e+03 7.21e-02 1.30e+02 pdb=" CG TRP H 36 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " 0.133 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " -0.061 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " 0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " -0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " 0.093 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " 0.010 2.00e-02 2.50e+03 ... (remaining 754 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1963 2.94 - 3.43: 4006 3.43 - 3.92: 6630 3.92 - 4.41: 7440 4.41 - 4.90: 12962 Nonbonded interactions: 33001 Sorted by model distance: nonbonded pdb=" O SER H 212 " pdb=" OD1 ASN H 213 " model vdw 2.448 3.040 nonbonded pdb=" N VAL H 220 " pdb=" O VAL H 220 " model vdw 2.462 2.496 nonbonded pdb=" OG1 THR H 202 " pdb=" O VAL H 220 " model vdw 2.464 3.040 nonbonded pdb=" O ASP E 132 " pdb=" OD1 ASP E 132 " model vdw 2.471 3.040 nonbonded pdb=" O CYS H 205 " pdb=" OD1 ASP H 217 " model vdw 2.484 3.040 ... (remaining 32996 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.190 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 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 : 0.028 0.143 4355 Z= 1.775 Angle : 2.181 10.430 5917 Z= 1.451 Chirality : 0.167 0.614 660 Planarity : 0.024 0.096 757 Dihedral : 13.699 89.120 1576 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.19 % Twisted Proline : 6.90 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.33), residues: 549 helix: -2.95 (0.79), residues: 20 sheet: -1.83 (0.32), residues: 240 loop : -2.15 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.009 ARG E 96 TYR 0.118 0.033 TYR L 173 PHE 0.094 0.030 PHE L 118 TRP 0.169 0.055 TRP H 163 HIS 0.085 0.042 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.02786 ( 4349) covalent geometry : angle 2.16187 ( 5905) SS BOND : bond 0.05126 ( 6) SS BOND : angle 6.72118 ( 12) hydrogen bonds : bond 0.17552 ( 127) hydrogen bonds : angle 9.04641 ( 315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: E 123 LYS cc_start: 0.7852 (mtpt) cc_final: 0.7500 (mtpt) REVERT: H 10 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7972 (mt-10) REVERT: H 12 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7878 (mmmt) REVERT: H 50 GLU cc_start: 0.7647 (pt0) cc_final: 0.7066 (pt0) REVERT: H 90 ASP cc_start: 0.7671 (m-30) cc_final: 0.7244 (m-30) REVERT: H 208 ASN cc_start: 0.7612 (t0) cc_final: 0.7090 (t0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0797 time to fit residues: 9.3685 Evaluate side-chains 78 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.0070 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 HIS H 39 GLN ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.166108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144345 restraints weight = 6062.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144430 restraints weight = 4733.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.145942 restraints weight = 4324.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.147073 restraints weight = 3060.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.147385 restraints weight = 2628.054| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4355 Z= 0.151 Angle : 0.698 8.387 5917 Z= 0.368 Chirality : 0.045 0.164 660 Planarity : 0.005 0.052 757 Dihedral : 5.917 22.022 596 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.26 % Allowed : 5.24 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.36), residues: 549 helix: -1.26 (1.08), residues: 16 sheet: -1.35 (0.34), residues: 231 loop : -1.73 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 211 TYR 0.021 0.002 TYR H 33 PHE 0.017 0.002 PHE L 209 TRP 0.021 0.002 TRP H 47 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4349) covalent geometry : angle 0.69523 ( 5905) SS BOND : bond 0.00411 ( 6) SS BOND : angle 1.62035 ( 12) hydrogen bonds : bond 0.03836 ( 127) hydrogen bonds : angle 6.93430 ( 315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: E 123 LYS cc_start: 0.7483 (mtpt) cc_final: 0.7250 (mtpt) REVERT: H 90 ASP cc_start: 0.7436 (m-30) cc_final: 0.7223 (m-30) REVERT: H 114 GLN cc_start: 0.6550 (mm-40) cc_final: 0.6276 (mm-40) REVERT: H 208 ASN cc_start: 0.7571 (t0) cc_final: 0.6775 (t0) REVERT: L 139 PHE cc_start: 0.8392 (p90) cc_final: 0.8180 (p90) outliers start: 6 outliers final: 2 residues processed: 85 average time/residue: 0.0718 time to fit residues: 7.8913 Evaluate side-chains 79 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 0.0670 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 89 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 = 0.4093 r_free = 0.4093 target = 0.166325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143852 restraints weight = 5955.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143673 restraints weight = 4312.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145169 restraints weight = 4034.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145833 restraints weight = 2869.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146448 restraints weight = 2600.444| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4355 Z= 0.144 Angle : 0.642 8.341 5917 Z= 0.339 Chirality : 0.044 0.162 660 Planarity : 0.005 0.049 757 Dihedral : 5.307 20.134 596 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.10 % Allowed : 8.60 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.37), residues: 549 helix: -0.33 (1.20), residues: 16 sheet: -1.23 (0.34), residues: 242 loop : -1.47 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 96 TYR 0.016 0.002 TYR H 33 PHE 0.008 0.001 PHE L 139 TRP 0.014 0.002 TRP L 148 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4349) covalent geometry : angle 0.64114 ( 5905) SS BOND : bond 0.00665 ( 6) SS BOND : angle 1.02831 ( 12) hydrogen bonds : bond 0.03323 ( 127) hydrogen bonds : angle 6.49225 ( 315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: E 30 GLN cc_start: 0.7359 (tm-30) cc_final: 0.6944 (mm110) REVERT: E 123 LYS cc_start: 0.7474 (mtpt) cc_final: 0.7239 (mtpt) REVERT: H 90 ASP cc_start: 0.7436 (m-30) cc_final: 0.7185 (m-30) REVERT: H 114 GLN cc_start: 0.6666 (mm-40) cc_final: 0.6447 (mm-40) REVERT: H 208 ASN cc_start: 0.7673 (t0) cc_final: 0.7253 (t0) REVERT: H 210 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8089 (mmtm) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.0697 time to fit residues: 7.2761 Evaluate side-chains 84 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 89 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 = 0.4032 r_free = 0.4032 target = 0.161069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135743 restraints weight = 5953.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138739 restraints weight = 3666.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140772 restraints weight = 2585.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142270 restraints weight = 2011.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143126 restraints weight = 1671.488| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4355 Z= 0.209 Angle : 0.689 8.861 5917 Z= 0.365 Chirality : 0.045 0.148 660 Planarity : 0.005 0.054 757 Dihedral : 5.541 24.082 596 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 3.14 % Allowed : 8.39 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.37), residues: 549 helix: -0.59 (1.07), residues: 16 sheet: -1.45 (0.32), residues: 262 loop : -1.40 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 211 TYR 0.017 0.002 TYR H 33 PHE 0.010 0.002 PHE L 139 TRP 0.016 0.002 TRP L 148 HIS 0.004 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 4349) covalent geometry : angle 0.68836 ( 5905) SS BOND : bond 0.00516 ( 6) SS BOND : angle 1.10378 ( 12) hydrogen bonds : bond 0.03718 ( 127) hydrogen bonds : angle 6.59648 ( 315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.163 Fit side-chains REVERT: E 123 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7529 (mtpt) REVERT: H 114 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6686 (mm-40) REVERT: H 156 PRO cc_start: 0.7543 (Cg_endo) cc_final: 0.7052 (Cg_exo) REVERT: H 208 ASN cc_start: 0.7747 (t0) cc_final: 0.7084 (t0) REVERT: H 210 LYS cc_start: 0.8439 (mmtt) cc_final: 0.7987 (mmtm) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.0630 time to fit residues: 7.0042 Evaluate side-chains 88 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 89 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 = 0.4054 r_free = 0.4054 target = 0.162811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140300 restraints weight = 6015.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140809 restraints weight = 4340.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141507 restraints weight = 3561.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142111 restraints weight = 3136.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143080 restraints weight = 2692.302| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4355 Z= 0.158 Angle : 0.646 8.173 5917 Z= 0.341 Chirality : 0.044 0.167 660 Planarity : 0.004 0.055 757 Dihedral : 5.235 21.438 596 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.73 % Allowed : 9.22 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.37), residues: 549 helix: -0.35 (1.10), residues: 16 sheet: -1.35 (0.33), residues: 258 loop : -1.35 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 142 TYR 0.014 0.002 TYR H 33 PHE 0.009 0.001 PHE E 55 TRP 0.016 0.002 TRP L 148 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4349) covalent geometry : angle 0.64504 ( 5905) SS BOND : bond 0.00513 ( 6) SS BOND : angle 1.10280 ( 12) hydrogen bonds : bond 0.03239 ( 127) hydrogen bonds : angle 6.32748 ( 315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: E 30 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6836 (mm-40) REVERT: E 123 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7494 (mtpt) REVERT: H 156 PRO cc_start: 0.7462 (Cg_endo) cc_final: 0.7005 (Cg_exo) REVERT: H 208 ASN cc_start: 0.7676 (t0) cc_final: 0.7110 (t0) REVERT: H 210 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7975 (mmtm) outliers start: 13 outliers final: 8 residues processed: 85 average time/residue: 0.0579 time to fit residues: 6.5833 Evaluate side-chains 87 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 38 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143682 restraints weight = 6048.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143740 restraints weight = 4396.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144783 restraints weight = 4044.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145382 restraints weight = 3133.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145892 restraints weight = 2778.643| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4355 Z= 0.117 Angle : 0.615 8.243 5917 Z= 0.322 Chirality : 0.043 0.143 660 Planarity : 0.004 0.049 757 Dihedral : 4.855 20.975 596 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.73 % Allowed : 10.06 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.38), residues: 549 helix: 0.12 (1.21), residues: 16 sheet: -1.22 (0.34), residues: 250 loop : -1.20 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 142 TYR 0.013 0.001 TYR H 154 PHE 0.006 0.001 PHE H 175 TRP 0.016 0.002 TRP L 148 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4349) covalent geometry : angle 0.61360 ( 5905) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.17423 ( 12) hydrogen bonds : bond 0.02955 ( 127) hydrogen bonds : angle 6.06936 ( 315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: E 123 LYS cc_start: 0.7522 (mtpt) cc_final: 0.7317 (mtpt) REVERT: H 156 PRO cc_start: 0.7426 (Cg_endo) cc_final: 0.6998 (Cg_exo) REVERT: H 208 ASN cc_start: 0.7614 (t0) cc_final: 0.6917 (t0) REVERT: H 210 LYS cc_start: 0.8388 (mmtt) cc_final: 0.7907 (mmtm) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 0.0669 time to fit residues: 7.8803 Evaluate side-chains 89 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 38 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.165728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140195 restraints weight = 6027.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143330 restraints weight = 3678.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145520 restraints weight = 2552.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.146975 restraints weight = 1966.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148095 restraints weight = 1623.052| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4355 Z= 0.118 Angle : 0.626 8.517 5917 Z= 0.327 Chirality : 0.043 0.169 660 Planarity : 0.004 0.052 757 Dihedral : 4.642 19.433 596 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.31 % Allowed : 11.74 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.38), residues: 549 helix: 0.31 (1.26), residues: 16 sheet: -1.13 (0.34), residues: 250 loop : -1.14 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 211 TYR 0.014 0.001 TYR H 33 PHE 0.008 0.001 PHE L 71 TRP 0.019 0.002 TRP L 148 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4349) covalent geometry : angle 0.62488 ( 5905) SS BOND : bond 0.00448 ( 6) SS BOND : angle 1.10024 ( 12) hydrogen bonds : bond 0.02785 ( 127) hydrogen bonds : angle 5.93718 ( 315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: E 30 GLN cc_start: 0.6946 (tm-30) cc_final: 0.6698 (mm-40) REVERT: H 156 PRO cc_start: 0.7518 (Cg_endo) cc_final: 0.7067 (Cg_exo) REVERT: H 208 ASN cc_start: 0.7673 (t0) cc_final: 0.6897 (t0) REVERT: H 210 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7732 (mmtm) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.0670 time to fit residues: 7.8180 Evaluate side-chains 89 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 22 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 173 HIS ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.167116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141496 restraints weight = 5930.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144602 restraints weight = 3629.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146864 restraints weight = 2540.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148339 restraints weight = 1947.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.149548 restraints weight = 1595.639| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4355 Z= 0.120 Angle : 0.633 8.279 5917 Z= 0.331 Chirality : 0.043 0.141 660 Planarity : 0.004 0.048 757 Dihedral : 4.612 19.021 596 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.73 % Allowed : 12.79 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.38), residues: 549 helix: 0.43 (1.27), residues: 16 sheet: -0.99 (0.35), residues: 234 loop : -1.26 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 94 TYR 0.018 0.001 TYR H 33 PHE 0.017 0.001 PHE L 209 TRP 0.016 0.002 TRP L 148 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4349) covalent geometry : angle 0.63170 ( 5905) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.14755 ( 12) hydrogen bonds : bond 0.02825 ( 127) hydrogen bonds : angle 5.88395 ( 315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: E 30 GLN cc_start: 0.6928 (tm-30) cc_final: 0.6693 (mm-40) REVERT: E 34 LEU cc_start: 0.7841 (mt) cc_final: 0.7637 (mp) REVERT: H 156 PRO cc_start: 0.7670 (Cg_endo) cc_final: 0.7239 (Cg_exo) REVERT: H 208 ASN cc_start: 0.7690 (t0) cc_final: 0.6845 (t0) REVERT: H 210 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7728 (mmtm) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.0700 time to fit residues: 7.3739 Evaluate side-chains 87 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.0050 chunk 24 optimal weight: 0.4980 chunk 27 optimal weight: 0.0570 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 7 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.1368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.171476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.149554 restraints weight = 5941.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150263 restraints weight = 4053.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.151875 restraints weight = 3695.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.152269 restraints weight = 2717.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.153107 restraints weight = 2338.566| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4355 Z= 0.111 Angle : 0.645 10.533 5917 Z= 0.331 Chirality : 0.043 0.155 660 Planarity : 0.004 0.048 757 Dihedral : 4.319 17.804 596 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.89 % Allowed : 12.58 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.38), residues: 549 helix: 0.63 (1.35), residues: 16 sheet: -0.97 (0.35), residues: 238 loop : -1.09 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 211 TYR 0.015 0.001 TYR H 33 PHE 0.013 0.001 PHE L 209 TRP 0.018 0.002 TRP L 148 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4349) covalent geometry : angle 0.64358 ( 5905) SS BOND : bond 0.00390 ( 6) SS BOND : angle 1.16627 ( 12) hydrogen bonds : bond 0.02646 ( 127) hydrogen bonds : angle 5.64860 ( 315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.164 Fit side-chains REVERT: E 30 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6808 (mm-40) REVERT: E 34 LEU cc_start: 0.7784 (mt) cc_final: 0.7565 (mp) REVERT: E 123 LYS cc_start: 0.7123 (mtpt) cc_final: 0.6915 (mtpt) REVERT: H 156 PRO cc_start: 0.7330 (Cg_endo) cc_final: 0.6979 (Cg_exo) REVERT: H 208 ASN cc_start: 0.7522 (t0) cc_final: 0.6753 (t0) REVERT: H 210 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7783 (mmtm) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.0610 time to fit residues: 7.1918 Evaluate side-chains 87 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 173 HIS H 209 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.164894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138697 restraints weight = 5983.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141747 restraints weight = 3755.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143671 restraints weight = 2672.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145374 restraints weight = 2101.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.146551 restraints weight = 1737.700| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4355 Z= 0.177 Angle : 0.695 9.752 5917 Z= 0.360 Chirality : 0.044 0.134 660 Planarity : 0.005 0.051 757 Dihedral : 4.775 19.926 596 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.89 % Allowed : 13.84 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.38), residues: 549 helix: 0.31 (1.23), residues: 16 sheet: -1.06 (0.33), residues: 253 loop : -1.20 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.022 0.002 TYR H 33 PHE 0.014 0.002 PHE L 209 TRP 0.022 0.002 TRP L 148 HIS 0.004 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4349) covalent geometry : angle 0.69414 ( 5905) SS BOND : bond 0.00529 ( 6) SS BOND : angle 1.13991 ( 12) hydrogen bonds : bond 0.03206 ( 127) hydrogen bonds : angle 5.94727 ( 315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: H 109 MET cc_start: 0.7809 (mpp) cc_final: 0.7380 (mtm) REVERT: H 156 PRO cc_start: 0.7752 (Cg_endo) cc_final: 0.7447 (Cg_exo) REVERT: H 208 ASN cc_start: 0.7732 (t0) cc_final: 0.6801 (t0) REVERT: H 210 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7674 (mmtm) REVERT: L 49 TYR cc_start: 0.6012 (p90) cc_final: 0.5697 (p90) REVERT: L 142 ARG cc_start: 0.6621 (tpp-160) cc_final: 0.6372 (ttm110) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.0668 time to fit residues: 6.8739 Evaluate side-chains 79 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 173 HIS L 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137723 restraints weight = 5988.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140615 restraints weight = 3779.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142702 restraints weight = 2687.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144111 restraints weight = 2091.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145127 restraints weight = 1741.343| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4355 Z= 0.172 Angle : 0.704 9.852 5917 Z= 0.364 Chirality : 0.045 0.159 660 Planarity : 0.004 0.052 757 Dihedral : 4.960 20.120 596 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.89 % Allowed : 13.63 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.37), residues: 549 helix: 0.06 (1.18), residues: 16 sheet: -1.12 (0.33), residues: 250 loop : -1.28 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 211 TYR 0.024 0.002 TYR H 33 PHE 0.012 0.002 PHE L 209 TRP 0.027 0.002 TRP L 148 HIS 0.001 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4349) covalent geometry : angle 0.70234 ( 5905) SS BOND : bond 0.00533 ( 6) SS BOND : angle 1.14110 ( 12) hydrogen bonds : bond 0.03192 ( 127) hydrogen bonds : angle 6.09267 ( 315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 935.09 seconds wall clock time: 16 minutes 56.61 seconds (1016.61 seconds total)