Starting phenix.real_space_refine on Wed Mar 12 21:30:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hik_34819/03_2025/8hik_34819.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hik_34819/03_2025/8hik_34819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hik_34819/03_2025/8hik_34819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hik_34819/03_2025/8hik_34819.map" model { file = "/net/cci-nas-00/data/ceres_data/8hik_34819/03_2025/8hik_34819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hik_34819/03_2025/8hik_34819.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 5296 2.51 5 N 1376 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'TPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.63 Number of scatterers: 8238 At special positions: 0 Unit cell: (66.34, 99.51, 148.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1537 8.00 N 1376 7.00 C 5296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 941.9 milliseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid -80 through -64 removed outlier: 3.672A pdb=" N LYS A -64 " --> pdb=" O LYS A -68 " (cutoff:3.500A) Processing helix chain 'A' and resid -57 through -43 removed outlier: 3.598A pdb=" N ALA A -43 " --> pdb=" O ALA A -47 " (cutoff:3.500A) Processing helix chain 'A' and resid -38 through -33 removed outlier: 4.020A pdb=" N ASP A -33 " --> pdb=" O PRO A -37 " (cutoff:3.500A) Processing helix chain 'A' and resid -25 through -3 removed outlier: 3.702A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.694A pdb=" N ALA A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.114A pdb=" N LEU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.884A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.115A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 202 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 264 through 296 removed outlier: 3.936A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.718A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 418 Processing helix chain 'A' and resid 427 through 451 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.532A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.631A pdb=" N LYS H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.097A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.588A pdb=" N VAL H 15 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.145A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.145A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.332A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.735A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.833A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR N 115 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR N 94 " --> pdb=" O THR N 115 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.833A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR N 115 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR N 94 " --> pdb=" O THR N 115 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR N 110 " --> pdb=" O ILE N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 13 through 14 Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.941A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.941A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.961A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 147 through 148 446 hydrogen bonds defined for protein. 1248 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: 2.40 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2562 1.34 - 1.46: 2030 1.46 - 1.58: 3807 1.58 - 1.70: 3 1.70 - 1.81: 38 Bond restraints: 8440 Sorted by residual: bond pdb=" C5 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 1.727 1.510 0.217 1.00e-02 1.00e+04 4.69e+02 bond pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 1.675 1.544 0.131 1.00e-02 1.00e+04 1.71e+02 bond pdb=" C4' TPP A 601 " pdb=" N4' TPP A 601 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" C2 TPP A 601 " pdb=" N3 TPP A 601 " ideal model delta sigma weight residual 1.318 1.424 -0.106 1.30e-02 5.92e+03 6.66e+01 bond pdb=" O3A TPP A 601 " pdb=" PB TPP A 601 " ideal model delta sigma weight residual 1.587 1.662 -0.075 1.10e-02 8.26e+03 4.66e+01 ... (remaining 8435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 11372 3.25 - 6.49: 91 6.49 - 9.74: 18 9.74 - 12.98: 2 12.98 - 16.23: 1 Bond angle restraints: 11484 Sorted by residual: angle pdb=" PA TPP A 601 " pdb=" O3A TPP A 601 " pdb=" PB TPP A 601 " ideal model delta sigma weight residual 139.87 123.64 16.23 1.00e+00 1.00e+00 2.63e+02 angle pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " pdb=" C5 TPP A 601 " ideal model delta sigma weight residual 91.33 104.13 -12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" C7 TPP A 601 " pdb=" O7 TPP A 601 " pdb=" PA TPP A 601 " ideal model delta sigma weight residual 124.29 118.57 5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" N1' TPP A 601 " pdb=" C2' TPP A 601 " pdb=" N3' TPP A 601 " ideal model delta sigma weight residual 125.71 119.88 5.83 1.07e+00 8.80e-01 2.99e+01 angle pdb=" N3 TPP A 601 " pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 112.34 107.32 5.02 1.00e+00 1.00e+00 2.52e+01 ... (remaining 11479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4807 16.52 - 33.03: 110 33.03 - 49.54: 38 49.54 - 66.06: 1 66.06 - 82.57: 11 Dihedral angle restraints: 4967 sinusoidal: 1890 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 175.57 -82.57 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual -86.00 -120.31 34.31 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 957 0.049 - 0.097: 267 0.097 - 0.146: 64 0.146 - 0.195: 7 0.195 - 0.243: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA TYR N 104 " pdb=" N TYR N 104 " pdb=" C TYR N 104 " pdb=" CB TYR N 104 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 1293 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.016 2.00e-02 2.50e+03 1.51e-02 5.66e+00 pdb=" CG TRP H 102 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP H 105 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO H 106 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 106 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 106 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.035 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO H 109 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.030 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2236 2.81 - 3.33: 7133 3.33 - 3.85: 13492 3.85 - 4.38: 15090 4.38 - 4.90: 26545 Nonbonded interactions: 64496 Sorted by model distance: nonbonded pdb=" OG SER A 168 " pdb=" O GLY A 307 " model vdw 2.282 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.326 3.040 nonbonded pdb=" O GLU A -26 " pdb=" OH TYR A 22 " model vdw 2.336 3.040 nonbonded pdb=" NE ARG A -49 " pdb=" O LEU L 93 " model vdw 2.340 3.120 nonbonded pdb=" O TRP H 111 " pdb=" OH TYR L 92 " model vdw 2.345 3.040 ... (remaining 64491 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 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 : 0.005 0.217 8440 Z= 0.324 Angle : 0.820 16.228 11484 Z= 0.473 Chirality : 0.047 0.243 1296 Planarity : 0.006 0.058 1437 Dihedral : 9.567 75.327 2980 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.21), residues: 1045 helix: -1.96 (0.20), residues: 380 sheet: -1.92 (0.29), residues: 241 loop : -2.84 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 102 HIS 0.006 0.002 HIS H 38 PHE 0.029 0.002 PHE A 103 TYR 0.023 0.002 TYR H 53 ARG 0.006 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7460 (tttt) cc_final: 0.7258 (mtmm) REVERT: A -50 MET cc_start: 0.6245 (mmm) cc_final: 0.5921 (mmm) REVERT: A -22 PHE cc_start: 0.7319 (t80) cc_final: 0.6815 (t80) REVERT: A 27 HIS cc_start: 0.5170 (m90) cc_final: 0.4851 (m-70) REVERT: A 73 SER cc_start: 0.6585 (m) cc_final: 0.6352 (t) REVERT: A 140 ILE cc_start: 0.7951 (mt) cc_final: 0.7742 (tp) REVERT: A 281 TYR cc_start: 0.6510 (t80) cc_final: 0.6203 (t80) REVERT: A 304 VAL cc_start: 0.7185 (t) cc_final: 0.5916 (m) REVERT: A 386 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7062 (tm-30) REVERT: A 387 ILE cc_start: 0.7155 (mt) cc_final: 0.6955 (mt) REVERT: H 86 MET cc_start: 0.6378 (mtm) cc_final: 0.6146 (mtm) REVERT: H 99 CYS cc_start: 0.5632 (t) cc_final: 0.5367 (t) REVERT: H 112 LYS cc_start: 0.7716 (mttt) cc_final: 0.7507 (ttmm) REVERT: H 119 GLN cc_start: 0.6958 (mt0) cc_final: 0.6698 (mt0) REVERT: H 135 VAL cc_start: 0.7872 (t) cc_final: 0.7591 (m) REVERT: H 136 PHE cc_start: 0.7525 (m-80) cc_final: 0.7085 (m-80) REVERT: N 34 MET cc_start: 0.6441 (mtp) cc_final: 0.6215 (mtp) REVERT: L 32 SER cc_start: 0.7747 (t) cc_final: 0.7452 (p) REVERT: L 37 TYR cc_start: 0.8263 (m-10) cc_final: 0.7688 (m-80) REVERT: L 43 LYS cc_start: 0.8431 (mttt) cc_final: 0.8094 (ttmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1944 time to fit residues: 58.1085 Evaluate side-chains 184 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -77 ASN A -42 GLN A 27 HIS A 120 GLN A 289 HIS A 293 ASN A 358 HIS H 178 HIS H 214 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 39 GLN L 90 GLN L 162 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.169791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.150903 restraints weight = 13073.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154780 restraints weight = 7268.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.157258 restraints weight = 4594.109| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 8440 Z= 0.270 Angle : 0.632 7.615 11484 Z= 0.330 Chirality : 0.042 0.178 1296 Planarity : 0.005 0.050 1437 Dihedral : 5.393 52.787 1163 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.35 % Allowed : 9.74 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.25), residues: 1045 helix: -0.28 (0.25), residues: 389 sheet: -1.46 (0.31), residues: 240 loop : -2.31 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP H 102 HIS 0.005 0.001 HIS H 38 PHE 0.017 0.002 PHE L 211 TYR 0.033 0.002 TYR A 126 ARG 0.011 0.001 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7770 (tttt) cc_final: 0.7379 (mtmm) REVERT: A -50 MET cc_start: 0.6545 (mmm) cc_final: 0.6275 (mmm) REVERT: A 27 HIS cc_start: 0.5967 (m-70) cc_final: 0.5711 (m-70) REVERT: A 73 SER cc_start: 0.7516 (m) cc_final: 0.7146 (t) REVERT: A 99 GLN cc_start: 0.7877 (tt0) cc_final: 0.7471 (tt0) REVERT: A 294 GLU cc_start: 0.6893 (tt0) cc_final: 0.6648 (tt0) REVERT: A 386 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7056 (tm-30) REVERT: A 387 ILE cc_start: 0.7121 (mt) cc_final: 0.6805 (mt) REVERT: H 7 LEU cc_start: 0.7566 (mm) cc_final: 0.7323 (mt) REVERT: H 46 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8149 (mmmm) REVERT: H 63 TYR cc_start: 0.7718 (m-10) cc_final: 0.7314 (m-10) REVERT: H 86 MET cc_start: 0.6779 (mtm) cc_final: 0.6529 (mtm) REVERT: H 135 VAL cc_start: 0.7889 (t) cc_final: 0.7583 (m) REVERT: H 136 PHE cc_start: 0.7615 (m-80) cc_final: 0.7330 (m-80) REVERT: H 168 TRP cc_start: 0.7218 (m100) cc_final: 0.6613 (m100) REVERT: H 197 THR cc_start: 0.7189 (p) cc_final: 0.6948 (p) REVERT: N 59 PHE cc_start: 0.7095 (m-80) cc_final: 0.6786 (m-80) REVERT: L 36 TRP cc_start: 0.8135 (m100) cc_final: 0.7816 (m100) REVERT: L 43 LYS cc_start: 0.8653 (mttt) cc_final: 0.8364 (mmmm) REVERT: L 47 LEU cc_start: 0.8576 (tp) cc_final: 0.8293 (tt) REVERT: L 87 TYR cc_start: 0.8419 (m-80) cc_final: 0.8041 (m-10) REVERT: L 104 THR cc_start: 0.7800 (p) cc_final: 0.7500 (p) REVERT: L 117 VAL cc_start: 0.8237 (t) cc_final: 0.7934 (p) REVERT: L 166 THR cc_start: 0.8479 (t) cc_final: 0.8002 (m) outliers start: 21 outliers final: 10 residues processed: 233 average time/residue: 0.1870 time to fit residues: 61.1681 Evaluate side-chains 213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 0.6980 chunk 93 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 95 optimal weight: 0.0470 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.0010 overall best weight: 0.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -20 HIS A 293 ASN A 377 GLN L 160 ASN L 168 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.173676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.155110 restraints weight = 13297.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158788 restraints weight = 7399.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.161266 restraints weight = 4684.586| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8440 Z= 0.153 Angle : 0.575 7.793 11484 Z= 0.285 Chirality : 0.041 0.152 1296 Planarity : 0.004 0.081 1437 Dihedral : 5.068 54.567 1163 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.90 % Allowed : 12.77 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.26), residues: 1045 helix: 0.43 (0.26), residues: 385 sheet: -1.15 (0.32), residues: 243 loop : -2.18 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 117 HIS 0.002 0.001 HIS A 355 PHE 0.017 0.001 PHE A 212 TYR 0.022 0.002 TYR A 126 ARG 0.007 0.000 ARG A -49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8148 (tttt) cc_final: 0.7914 (ttpt) REVERT: A -51 LYS cc_start: 0.7523 (tttt) cc_final: 0.7268 (mtmm) REVERT: A -49 ARG cc_start: 0.7690 (tpt-90) cc_final: 0.7458 (tpp80) REVERT: A 67 GLU cc_start: 0.7801 (tt0) cc_final: 0.7584 (tt0) REVERT: A 73 SER cc_start: 0.7315 (m) cc_final: 0.7047 (t) REVERT: A 99 GLN cc_start: 0.7709 (tt0) cc_final: 0.7480 (tt0) REVERT: A 150 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7377 (tp40) REVERT: A 386 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7046 (tm-30) REVERT: H 20 SER cc_start: 0.7741 (m) cc_final: 0.7314 (p) REVERT: H 46 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8141 (mmmm) REVERT: H 86 MET cc_start: 0.6692 (mtm) cc_final: 0.6290 (mtm) REVERT: H 110 TRP cc_start: 0.7944 (t60) cc_final: 0.6779 (t60) REVERT: H 116 TYR cc_start: 0.7205 (m-10) cc_final: 0.6926 (m-80) REVERT: H 135 VAL cc_start: 0.7887 (t) cc_final: 0.7521 (m) REVERT: H 136 PHE cc_start: 0.7639 (m-80) cc_final: 0.7350 (m-80) REVERT: N 59 PHE cc_start: 0.6945 (m-80) cc_final: 0.6640 (m-80) REVERT: L 36 TRP cc_start: 0.7930 (m100) cc_final: 0.7669 (m100) REVERT: L 43 LYS cc_start: 0.8612 (mttt) cc_final: 0.8387 (mmmm) REVERT: L 47 LEU cc_start: 0.8470 (tp) cc_final: 0.8247 (tt) REVERT: L 48 LEU cc_start: 0.8025 (tp) cc_final: 0.7722 (tp) REVERT: L 74 LEU cc_start: 0.8215 (tt) cc_final: 0.7998 (tp) REVERT: L 87 TYR cc_start: 0.8353 (m-80) cc_final: 0.7902 (m-80) outliers start: 17 outliers final: 8 residues processed: 208 average time/residue: 0.1820 time to fit residues: 53.0089 Evaluate side-chains 194 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 186 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 0.0270 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -77 ASN A 277 ASN H 169 ASN L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.165949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147042 restraints weight = 13163.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.150914 restraints weight = 7119.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.153457 restraints weight = 4445.557| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8440 Z= 0.261 Angle : 0.635 9.630 11484 Z= 0.319 Chirality : 0.042 0.130 1296 Planarity : 0.004 0.071 1437 Dihedral : 5.100 49.248 1163 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.35 % Allowed : 14.00 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1045 helix: 0.37 (0.26), residues: 389 sheet: -0.88 (0.32), residues: 242 loop : -2.04 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 102 HIS 0.004 0.001 HIS A -20 PHE 0.015 0.001 PHE L 211 TYR 0.023 0.002 TYR A 126 ARG 0.007 0.001 ARG A -49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8278 (tttt) cc_final: 0.8022 (ttpt) REVERT: A -51 LYS cc_start: 0.7582 (tttt) cc_final: 0.7313 (mtmm) REVERT: A -49 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7338 (tpp80) REVERT: A 28 LEU cc_start: 0.7890 (mm) cc_final: 0.7364 (mp) REVERT: A 71 VAL cc_start: 0.7543 (m) cc_final: 0.7332 (p) REVERT: A 73 SER cc_start: 0.7967 (m) cc_final: 0.7497 (t) REVERT: A 99 GLN cc_start: 0.7682 (tt0) cc_final: 0.7237 (tt0) REVERT: A 294 GLU cc_start: 0.6891 (tt0) cc_final: 0.6656 (tt0) REVERT: A 386 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7081 (tp40) REVERT: H 20 SER cc_start: 0.8119 (m) cc_final: 0.7758 (p) REVERT: H 46 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8140 (mmmm) REVERT: H 63 TYR cc_start: 0.7710 (m-10) cc_final: 0.7331 (m-10) REVERT: H 110 TRP cc_start: 0.8189 (t60) cc_final: 0.6864 (t60) REVERT: H 116 TYR cc_start: 0.7703 (m-10) cc_final: 0.7471 (m-80) REVERT: H 135 VAL cc_start: 0.7883 (t) cc_final: 0.7607 (m) REVERT: H 136 PHE cc_start: 0.7743 (m-80) cc_final: 0.7521 (m-80) REVERT: N 39 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.4009 (mp10) REVERT: L 43 LYS cc_start: 0.8694 (mttt) cc_final: 0.8433 (mtpp) REVERT: L 48 LEU cc_start: 0.7966 (tp) cc_final: 0.7630 (tp) REVERT: L 91 GLN cc_start: 0.7772 (pp30) cc_final: 0.7491 (pp30) REVERT: L 166 THR cc_start: 0.8579 (t) cc_final: 0.8183 (m) outliers start: 21 outliers final: 17 residues processed: 208 average time/residue: 0.1950 time to fit residues: 56.1914 Evaluate side-chains 203 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.165590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147636 restraints weight = 12956.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151289 restraints weight = 7068.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153784 restraints weight = 4432.388| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 8440 Z= 0.228 Angle : 0.620 9.374 11484 Z= 0.311 Chirality : 0.042 0.154 1296 Planarity : 0.004 0.068 1437 Dihedral : 5.011 48.160 1163 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.46 % Allowed : 17.25 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.26), residues: 1045 helix: 0.57 (0.26), residues: 385 sheet: -0.93 (0.32), residues: 244 loop : -1.93 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A -76 HIS 0.004 0.001 HIS A 355 PHE 0.014 0.001 PHE A 103 TYR 0.022 0.002 TYR A 149 ARG 0.007 0.001 ARG A -49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8279 (tttt) cc_final: 0.8011 (ttpt) REVERT: A -51 LYS cc_start: 0.7600 (tttt) cc_final: 0.7351 (mtmm) REVERT: A -50 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.6284 (tmm) REVERT: A -49 ARG cc_start: 0.7799 (tpt-90) cc_final: 0.7014 (tpt-90) REVERT: A 71 VAL cc_start: 0.7652 (m) cc_final: 0.7348 (p) REVERT: A 73 SER cc_start: 0.7956 (m) cc_final: 0.7506 (t) REVERT: A 86 LEU cc_start: 0.7600 (tt) cc_final: 0.7366 (tp) REVERT: A 99 GLN cc_start: 0.7669 (tt0) cc_final: 0.7021 (tt0) REVERT: A 122 MET cc_start: 0.7168 (tmm) cc_final: 0.5938 (tmm) REVERT: A 294 GLU cc_start: 0.6888 (tt0) cc_final: 0.6640 (tt0) REVERT: A 373 ARG cc_start: 0.6611 (mmm-85) cc_final: 0.5757 (mmm-85) REVERT: A 386 GLN cc_start: 0.7479 (mm-40) cc_final: 0.6938 (tp40) REVERT: A 387 ILE cc_start: 0.7191 (mt) cc_final: 0.6919 (tp) REVERT: H 20 SER cc_start: 0.8112 (m) cc_final: 0.7753 (p) REVERT: H 46 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8139 (mmmm) REVERT: H 63 TYR cc_start: 0.7725 (m-10) cc_final: 0.7369 (m-10) REVERT: H 110 TRP cc_start: 0.8220 (t60) cc_final: 0.7021 (t60) REVERT: H 116 TYR cc_start: 0.7465 (m-10) cc_final: 0.7258 (m-80) REVERT: H 135 VAL cc_start: 0.7930 (t) cc_final: 0.7612 (m) REVERT: L 7 GLN cc_start: 0.7353 (tt0) cc_final: 0.7116 (tt0) REVERT: L 36 TRP cc_start: 0.8251 (m100) cc_final: 0.7800 (m100) REVERT: L 43 LYS cc_start: 0.8697 (mttt) cc_final: 0.8427 (mtpp) REVERT: L 47 LEU cc_start: 0.8551 (tp) cc_final: 0.8304 (tt) REVERT: L 48 LEU cc_start: 0.7902 (tp) cc_final: 0.7551 (tp) REVERT: L 91 GLN cc_start: 0.7190 (pp30) cc_final: 0.6963 (pp30) REVERT: L 92 TYR cc_start: 0.8353 (p90) cc_final: 0.7675 (p90) REVERT: L 166 THR cc_start: 0.8554 (t) cc_final: 0.8123 (m) outliers start: 22 outliers final: 15 residues processed: 207 average time/residue: 0.2219 time to fit residues: 64.3963 Evaluate side-chains 208 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN ** L 201 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 = 0.4089 r_free = 0.4089 target = 0.163693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.145848 restraints weight = 13035.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149464 restraints weight = 7064.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151848 restraints weight = 4397.880| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8440 Z= 0.234 Angle : 0.649 11.884 11484 Z= 0.320 Chirality : 0.042 0.154 1296 Planarity : 0.004 0.066 1437 Dihedral : 4.933 41.497 1163 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.80 % Allowed : 17.47 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1045 helix: 0.55 (0.26), residues: 388 sheet: -0.82 (0.32), residues: 241 loop : -1.90 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.027 0.001 PHE H 136 TYR 0.026 0.002 TYR A 126 ARG 0.005 0.000 ARG A -49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8309 (tttt) cc_final: 0.8046 (ttpt) REVERT: A -51 LYS cc_start: 0.7729 (tttt) cc_final: 0.7415 (mtmm) REVERT: A -49 ARG cc_start: 0.7804 (tpt-90) cc_final: 0.7015 (tpt-90) REVERT: A 53 LEU cc_start: 0.6405 (mp) cc_final: 0.5971 (mt) REVERT: A 71 VAL cc_start: 0.7484 (m) cc_final: 0.7150 (p) REVERT: A 73 SER cc_start: 0.8141 (m) cc_final: 0.7737 (t) REVERT: A 99 GLN cc_start: 0.7688 (tt0) cc_final: 0.7146 (tt0) REVERT: A 122 MET cc_start: 0.7221 (tmm) cc_final: 0.5858 (tmm) REVERT: A 264 ARG cc_start: 0.4555 (mtp85) cc_final: 0.4233 (mtm110) REVERT: A 294 GLU cc_start: 0.6908 (tt0) cc_final: 0.6650 (tt0) REVERT: A 300 ASN cc_start: 0.6053 (t0) cc_final: 0.5835 (t0) REVERT: A 366 TYR cc_start: 0.6804 (m-80) cc_final: 0.6274 (m-80) REVERT: A 373 ARG cc_start: 0.6743 (mmm-85) cc_final: 0.6150 (tpp80) REVERT: A 386 GLN cc_start: 0.7394 (mm-40) cc_final: 0.6983 (tp40) REVERT: A 387 ILE cc_start: 0.7174 (mt) cc_final: 0.6897 (tp) REVERT: H 20 SER cc_start: 0.8176 (m) cc_final: 0.7781 (p) REVERT: H 37 LEU cc_start: 0.7938 (mm) cc_final: 0.7640 (mt) REVERT: H 46 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8134 (mmmm) REVERT: H 63 TYR cc_start: 0.7750 (m-10) cc_final: 0.7427 (m-10) REVERT: H 110 TRP cc_start: 0.8284 (t60) cc_final: 0.6992 (t60) REVERT: L 7 GLN cc_start: 0.7316 (tt0) cc_final: 0.6877 (tt0) REVERT: L 36 TRP cc_start: 0.8302 (m100) cc_final: 0.7848 (m100) REVERT: L 48 LEU cc_start: 0.7967 (tp) cc_final: 0.7617 (tp) REVERT: L 91 GLN cc_start: 0.7248 (pp30) cc_final: 0.6880 (pp30) REVERT: L 92 TYR cc_start: 0.8338 (p90) cc_final: 0.7624 (p90) REVERT: L 142 TYR cc_start: 0.7553 (t80) cc_final: 0.7076 (t80) REVERT: L 166 THR cc_start: 0.8561 (t) cc_final: 0.8141 (m) outliers start: 25 outliers final: 19 residues processed: 223 average time/residue: 0.2694 time to fit residues: 81.3453 Evaluate side-chains 216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -26 GLU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN A 293 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138185 restraints weight = 13174.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141827 restraints weight = 7119.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144336 restraints weight = 4460.438| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 8440 Z= 0.319 Angle : 0.712 10.223 11484 Z= 0.354 Chirality : 0.044 0.157 1296 Planarity : 0.005 0.064 1437 Dihedral : 5.229 34.574 1163 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.58 % Allowed : 17.58 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1045 helix: 0.32 (0.26), residues: 389 sheet: -0.91 (0.33), residues: 240 loop : -1.84 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 168 HIS 0.005 0.001 HIS A 355 PHE 0.025 0.002 PHE H 136 TYR 0.026 0.002 TYR H 53 ARG 0.007 0.001 ARG A -49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8356 (tttt) cc_final: 0.8146 (ttpt) REVERT: A -51 LYS cc_start: 0.7712 (tttt) cc_final: 0.7386 (mtmm) REVERT: A -49 ARG cc_start: 0.7926 (tpt-90) cc_final: 0.7631 (tpp80) REVERT: A 46 SER cc_start: 0.7937 (m) cc_final: 0.7485 (t) REVERT: A 53 LEU cc_start: 0.6396 (mp) cc_final: 0.5939 (mt) REVERT: A 71 VAL cc_start: 0.7590 (m) cc_final: 0.7239 (p) REVERT: A 73 SER cc_start: 0.8224 (m) cc_final: 0.7847 (t) REVERT: A 99 GLN cc_start: 0.7698 (tt0) cc_final: 0.7188 (tt0) REVERT: A 122 MET cc_start: 0.7217 (tmm) cc_final: 0.5935 (tmm) REVERT: A 264 ARG cc_start: 0.4399 (mtp85) cc_final: 0.4081 (mtm110) REVERT: A 294 GLU cc_start: 0.6970 (tt0) cc_final: 0.6721 (tt0) REVERT: A 300 ASN cc_start: 0.6052 (t0) cc_final: 0.5842 (t0) REVERT: A 373 ARG cc_start: 0.6803 (mmm-85) cc_final: 0.6185 (ttm-80) REVERT: A 386 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6959 (tp40) REVERT: A 387 ILE cc_start: 0.7220 (mt) cc_final: 0.6949 (tp) REVERT: H 46 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8109 (mmmm) REVERT: H 63 TYR cc_start: 0.7764 (m-10) cc_final: 0.7485 (m-10) REVERT: H 110 TRP cc_start: 0.8368 (t60) cc_final: 0.7089 (t60) REVERT: N 83 MET cc_start: 0.6585 (ptm) cc_final: 0.6173 (ppp) REVERT: L 7 GLN cc_start: 0.7445 (tt0) cc_final: 0.7139 (tt0) REVERT: L 36 TRP cc_start: 0.8387 (m100) cc_final: 0.7893 (m100) REVERT: L 38 GLN cc_start: 0.8349 (tt0) cc_final: 0.8136 (tt0) REVERT: L 48 LEU cc_start: 0.7868 (tp) cc_final: 0.7407 (tp) REVERT: L 91 GLN cc_start: 0.7557 (pp30) cc_final: 0.7208 (pp30) REVERT: L 92 TYR cc_start: 0.8381 (p90) cc_final: 0.7717 (p90) REVERT: L 94 TYR cc_start: 0.7733 (t80) cc_final: 0.7500 (t80) REVERT: L 142 TYR cc_start: 0.7696 (t80) cc_final: 0.7208 (t80) REVERT: L 166 THR cc_start: 0.8570 (t) cc_final: 0.8192 (m) outliers start: 32 outliers final: 22 residues processed: 221 average time/residue: 0.2080 time to fit residues: 63.0194 Evaluate side-chains 226 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -26 GLU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.0050 chunk 12 optimal weight: 0.0370 chunk 87 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A -42 GLN A 293 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.164380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145729 restraints weight = 13342.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149548 restraints weight = 7262.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.152059 restraints weight = 4501.581| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8440 Z= 0.171 Angle : 0.653 9.901 11484 Z= 0.313 Chirality : 0.041 0.145 1296 Planarity : 0.004 0.064 1437 Dihedral : 4.826 38.170 1163 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.35 % Allowed : 19.82 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1045 helix: 0.54 (0.26), residues: 390 sheet: -0.78 (0.33), residues: 241 loop : -1.68 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.019 0.001 PHE H 136 TYR 0.025 0.002 TYR H 53 ARG 0.006 0.000 ARG A -21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.752 Fit side-chains REVERT: A -56 LYS cc_start: 0.8271 (tttt) cc_final: 0.8057 (ttpt) REVERT: A -51 LYS cc_start: 0.7635 (tttt) cc_final: 0.7275 (mtmm) REVERT: A -49 ARG cc_start: 0.7898 (tpt-90) cc_final: 0.7206 (tpp80) REVERT: A 40 GLN cc_start: 0.7797 (tp40) cc_final: 0.7423 (tp40) REVERT: A 42 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7170 (mtm110) REVERT: A 46 SER cc_start: 0.7942 (m) cc_final: 0.7476 (t) REVERT: A 53 LEU cc_start: 0.6419 (mp) cc_final: 0.6043 (mt) REVERT: A 71 VAL cc_start: 0.7472 (m) cc_final: 0.7135 (p) REVERT: A 73 SER cc_start: 0.8049 (m) cc_final: 0.7633 (t) REVERT: A 99 GLN cc_start: 0.7610 (tt0) cc_final: 0.7104 (tt0) REVERT: A 373 ARG cc_start: 0.6739 (mmm-85) cc_final: 0.6202 (ttm110) REVERT: A 386 GLN cc_start: 0.7444 (mm-40) cc_final: 0.6885 (mm110) REVERT: A 387 ILE cc_start: 0.7168 (mt) cc_final: 0.6872 (tp) REVERT: H 20 SER cc_start: 0.8083 (m) cc_final: 0.7711 (p) REVERT: H 37 LEU cc_start: 0.7898 (mm) cc_final: 0.7571 (mt) REVERT: H 46 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8144 (mmmm) REVERT: H 110 TRP cc_start: 0.8240 (t60) cc_final: 0.6883 (t60) REVERT: N 83 MET cc_start: 0.6498 (ptm) cc_final: 0.6162 (ppp) REVERT: L 36 TRP cc_start: 0.8259 (m100) cc_final: 0.7891 (m100) REVERT: L 48 LEU cc_start: 0.7946 (tp) cc_final: 0.7624 (tp) REVERT: L 74 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7875 (tt) REVERT: L 91 GLN cc_start: 0.7673 (pp30) cc_final: 0.7061 (pp30) REVERT: L 92 TYR cc_start: 0.8381 (p90) cc_final: 0.7770 (p90) REVERT: L 94 TYR cc_start: 0.7844 (t80) cc_final: 0.7603 (t80) REVERT: L 142 TYR cc_start: 0.7506 (t80) cc_final: 0.7016 (t80) outliers start: 21 outliers final: 17 residues processed: 208 average time/residue: 0.2980 time to fit residues: 86.4397 Evaluate side-chains 215 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -26 GLU Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 201 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 = 0.159349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140502 restraints weight = 13395.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144068 restraints weight = 7340.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.146549 restraints weight = 4660.308| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 8440 Z= 0.276 Angle : 0.703 11.237 11484 Z= 0.348 Chirality : 0.043 0.228 1296 Planarity : 0.005 0.062 1437 Dihedral : 5.099 29.239 1163 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.58 % Allowed : 20.16 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.26), residues: 1045 helix: 0.41 (0.26), residues: 389 sheet: -0.84 (0.33), residues: 249 loop : -1.65 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.026 0.002 PHE H 136 TYR 0.035 0.002 TYR A 149 ARG 0.005 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8262 (tttt) cc_final: 0.7996 (ttpt) REVERT: A -51 LYS cc_start: 0.7909 (tttt) cc_final: 0.7528 (mtmm) REVERT: A -49 ARG cc_start: 0.7766 (tpt-90) cc_final: 0.7543 (tpp80) REVERT: A 49 THR cc_start: 0.7362 (m) cc_final: 0.7031 (m) REVERT: A 53 LEU cc_start: 0.6414 (mp) cc_final: 0.5968 (mt) REVERT: A 73 SER cc_start: 0.7907 (m) cc_final: 0.7624 (t) REVERT: A 99 GLN cc_start: 0.7684 (tt0) cc_final: 0.7132 (tt0) REVERT: A 294 GLU cc_start: 0.6934 (tt0) cc_final: 0.6660 (tt0) REVERT: A 366 TYR cc_start: 0.7108 (m-80) cc_final: 0.6793 (m-80) REVERT: A 373 ARG cc_start: 0.6842 (mmm-85) cc_final: 0.5818 (tpp80) REVERT: A 386 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6795 (mm110) REVERT: A 387 ILE cc_start: 0.7139 (mt) cc_final: 0.6894 (tp) REVERT: H 37 LEU cc_start: 0.7948 (mm) cc_final: 0.7630 (mt) REVERT: H 84 LEU cc_start: 0.7214 (tp) cc_final: 0.6994 (tt) REVERT: H 110 TRP cc_start: 0.8365 (t60) cc_final: 0.6983 (t60) REVERT: L 38 GLN cc_start: 0.8312 (tt0) cc_final: 0.8107 (tt0) REVERT: L 92 TYR cc_start: 0.8385 (p90) cc_final: 0.7717 (p90) REVERT: L 94 TYR cc_start: 0.7858 (t80) cc_final: 0.7594 (t80) REVERT: L 142 TYR cc_start: 0.7562 (t80) cc_final: 0.7061 (t80) REVERT: L 166 THR cc_start: 0.8590 (t) cc_final: 0.8183 (m) outliers start: 23 outliers final: 17 residues processed: 218 average time/residue: 0.2098 time to fit residues: 62.6679 Evaluate side-chains 230 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -57 VAL Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 95 optimal weight: 0.1980 chunk 100 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 6 optimal weight: 0.1980 chunk 59 optimal weight: 0.1980 chunk 101 optimal weight: 0.6980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.164323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145450 restraints weight = 13218.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149237 restraints weight = 7213.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.151686 restraints weight = 4500.573| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8440 Z= 0.184 Angle : 0.686 10.349 11484 Z= 0.329 Chirality : 0.042 0.205 1296 Planarity : 0.005 0.063 1437 Dihedral : 4.860 30.577 1163 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.13 % Allowed : 21.28 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.26), residues: 1045 helix: 0.60 (0.27), residues: 390 sheet: -0.72 (0.33), residues: 243 loop : -1.62 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.025 0.001 PHE H 136 TYR 0.032 0.002 TYR A 149 ARG 0.004 0.000 ARG A 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8292 (tttt) cc_final: 0.8042 (ttpt) REVERT: A -51 LYS cc_start: 0.7845 (tttt) cc_final: 0.7483 (mtmm) REVERT: A -49 ARG cc_start: 0.7694 (tpt-90) cc_final: 0.7394 (tpp80) REVERT: A 49 THR cc_start: 0.7183 (m) cc_final: 0.6913 (m) REVERT: A 73 SER cc_start: 0.7645 (m) cc_final: 0.7339 (t) REVERT: A 99 GLN cc_start: 0.7607 (tt0) cc_final: 0.7059 (tt0) REVERT: A 264 ARG cc_start: 0.4569 (mtp85) cc_final: 0.4257 (ttm110) REVERT: A 373 ARG cc_start: 0.6805 (mmm-85) cc_final: 0.5995 (tpp80) REVERT: A 386 GLN cc_start: 0.7473 (mm-40) cc_final: 0.6902 (mm110) REVERT: A 387 ILE cc_start: 0.7117 (mt) cc_final: 0.6842 (tp) REVERT: H 20 SER cc_start: 0.8124 (m) cc_final: 0.7751 (p) REVERT: H 37 LEU cc_start: 0.7922 (mm) cc_final: 0.7628 (mt) REVERT: H 110 TRP cc_start: 0.8250 (t60) cc_final: 0.6911 (t60) REVERT: L 92 TYR cc_start: 0.8323 (p90) cc_final: 0.7940 (p90) REVERT: L 94 TYR cc_start: 0.7835 (t80) cc_final: 0.7634 (t80) REVERT: L 142 TYR cc_start: 0.7473 (t80) cc_final: 0.6905 (t80) outliers start: 19 outliers final: 12 residues processed: 212 average time/residue: 0.2416 time to fit residues: 70.4502 Evaluate side-chains 213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -57 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 88 optimal weight: 0.0470 chunk 1 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 overall best weight: 0.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 201 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 = 0.4089 r_free = 0.4089 target = 0.164078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.145113 restraints weight = 13337.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148943 restraints weight = 7272.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.151458 restraints weight = 4538.831| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8440 Z= 0.194 Angle : 0.675 10.626 11484 Z= 0.324 Chirality : 0.042 0.185 1296 Planarity : 0.004 0.061 1437 Dihedral : 4.787 28.983 1163 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.68 % Allowed : 21.84 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1045 helix: 0.71 (0.26), residues: 389 sheet: -0.54 (0.33), residues: 242 loop : -1.55 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.025 0.001 PHE H 136 TYR 0.040 0.002 TYR A 92 ARG 0.004 0.000 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3149.70 seconds wall clock time: 56 minutes 35.69 seconds (3395.69 seconds total)