Starting phenix.real_space_refine on Sat Jun 7 00:42:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hik_34819/06_2025/8hik_34819.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hik_34819/06_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_34819/06_2025/8hik_34819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hik_34819/06_2025/8hik_34819.map" model { file = "/net/cci-nas-00/data/ceres_data/8hik_34819/06_2025/8hik_34819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hik_34819/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.76, per 1000 atoms: 0.70 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 2.51 Time building geometry restraints manager: 2.72 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: 2.580 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- 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 8445 Z= 0.385 Angle : 0.821 16.228 11494 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 Details of bonding type rmsd hydrogen bonds : bond 0.11935 ( 420) hydrogen bonds : angle 6.64327 ( 1248) SS BOND : bond 0.00134 ( 5) SS BOND : angle 1.34217 ( 10) covalent geometry : bond 0.00515 ( 8440) covalent geometry : angle 0.82034 (11484) *********************** 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 : 0.820 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: 0.1889 time to fit residues: 56.4916 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 : 0.869 ------------------------------------------------------------------------------- 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 8445 Z= 0.201 Angle : 0.636 7.615 11494 Z= 0.331 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 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 420) hydrogen bonds : angle 5.42100 ( 1248) SS BOND : bond 0.00743 ( 5) SS BOND : angle 2.41035 ( 10) covalent geometry : bond 0.00430 ( 8440) covalent geometry : angle 0.63217 (11484) *********************** 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 : 0.828 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: 0.1785 time to fit residues: 58.1980 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 : 0.829 ------------------------------------------------------------------------------- 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: 0.1980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.0010 overall best weight: 0.1862 ------------------------------------------------------------------------------- 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 90 GLN L 160 ASN L 168 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.173033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154149 restraints weight = 13281.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.157872 restraints weight = 7357.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160415 restraints weight = 4664.655| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8445 Z= 0.117 Angle : 0.580 7.596 11494 Z= 0.288 Chirality : 0.041 0.156 1296 Planarity : 0.004 0.083 1437 Dihedral : 5.097 54.121 1163 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.02 % Allowed : 12.43 % Favored : 85.55 % 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: -1.50 (0.26), residues: 1045 helix: 0.39 (0.26), residues: 385 sheet: -1.16 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 420) hydrogen bonds : angle 4.95280 ( 1248) SS BOND : bond 0.00339 ( 5) SS BOND : angle 1.31608 ( 10) covalent geometry : bond 0.00253 ( 8440) covalent geometry : angle 0.57852 (11484) *********************** 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 213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8167 (tttt) cc_final: 0.7944 (ttpt) REVERT: A -51 LYS cc_start: 0.7560 (tttt) cc_final: 0.7301 (mtmm) REVERT: A -49 ARG cc_start: 0.7764 (tpt-90) cc_final: 0.7535 (tpp80) REVERT: A 73 SER cc_start: 0.7341 (m) cc_final: 0.7072 (t) REVERT: A 99 GLN cc_start: 0.7683 (tt0) cc_final: 0.7426 (tt0) REVERT: A 150 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7413 (tp40) REVERT: A 294 GLU cc_start: 0.6821 (tt0) cc_final: 0.6559 (tt0) REVERT: A 386 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7013 (tm-30) REVERT: H 20 SER cc_start: 0.7776 (m) cc_final: 0.7376 (p) REVERT: H 46 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8151 (mmmm) REVERT: H 86 MET cc_start: 0.6733 (mtm) cc_final: 0.6321 (mtm) REVERT: H 110 TRP cc_start: 0.7966 (t60) cc_final: 0.6823 (t60) REVERT: H 116 TYR cc_start: 0.7291 (m-10) cc_final: 0.7023 (m-80) REVERT: H 135 VAL cc_start: 0.7877 (t) cc_final: 0.7510 (m) REVERT: H 136 PHE cc_start: 0.7666 (m-80) cc_final: 0.7369 (m-80) REVERT: N 59 PHE cc_start: 0.6978 (m-80) cc_final: 0.6656 (m-80) REVERT: L 36 TRP cc_start: 0.7971 (m100) cc_final: 0.7603 (m100) REVERT: L 37 TYR cc_start: 0.8302 (m-80) cc_final: 0.7640 (m-80) REVERT: L 43 LYS cc_start: 0.8629 (mttt) cc_final: 0.8378 (mmmm) REVERT: L 47 LEU cc_start: 0.8492 (tp) cc_final: 0.8261 (tt) REVERT: L 48 LEU cc_start: 0.8019 (tp) cc_final: 0.7778 (tp) REVERT: L 74 LEU cc_start: 0.8222 (tt) cc_final: 0.7969 (tp) REVERT: L 87 TYR cc_start: 0.8384 (m-80) cc_final: 0.7790 (m-80) REVERT: L 90 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7728 (pt0) outliers start: 18 outliers final: 9 residues processed: 204 average time/residue: 0.1959 time to fit residues: 55.8707 Evaluate side-chains 197 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 440 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 89 CYS Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -77 ASN A 277 ASN H 169 ASN L 90 GLN L 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145070 restraints weight = 13288.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148865 restraints weight = 7241.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151482 restraints weight = 4594.661| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8445 Z= 0.211 Angle : 0.639 9.797 11494 Z= 0.325 Chirality : 0.042 0.142 1296 Planarity : 0.005 0.070 1437 Dihedral : 5.242 57.974 1163 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.46 % Allowed : 13.55 % Favored : 83.99 % 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: -1.42 (0.26), residues: 1045 helix: 0.31 (0.26), residues: 389 sheet: -1.01 (0.32), residues: 244 loop : -2.07 (0.30), residues: 412 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 0.024 0.002 TYR A 126 ARG 0.007 0.001 ARG A -49 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 420) hydrogen bonds : angle 5.26508 ( 1248) SS BOND : bond 0.00521 ( 5) SS BOND : angle 1.05712 ( 10) covalent geometry : bond 0.00448 ( 8440) covalent geometry : angle 0.63892 (11484) *********************** 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 226 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8297 (tttt) cc_final: 0.8034 (ttpt) REVERT: A -51 LYS cc_start: 0.7626 (tttt) cc_final: 0.7337 (mtmm) REVERT: A 71 VAL cc_start: 0.7533 (m) cc_final: 0.7307 (p) REVERT: A 73 SER cc_start: 0.8048 (m) cc_final: 0.7578 (t) REVERT: A 99 GLN cc_start: 0.7685 (tt0) cc_final: 0.7236 (tt0) REVERT: A 294 GLU cc_start: 0.6927 (tt0) cc_final: 0.6687 (tt0) REVERT: A 386 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7085 (tt0) REVERT: H 20 SER cc_start: 0.8120 (m) cc_final: 0.7776 (p) REVERT: H 46 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8156 (mmmm) REVERT: H 63 TYR cc_start: 0.7688 (m-10) cc_final: 0.7346 (m-10) REVERT: H 116 TYR cc_start: 0.7711 (m-10) cc_final: 0.7473 (m-80) REVERT: H 135 VAL cc_start: 0.7883 (t) cc_final: 0.7595 (m) REVERT: H 136 PHE cc_start: 0.7762 (m-80) cc_final: 0.7537 (m-80) REVERT: N 34 MET cc_start: 0.6228 (mtt) cc_final: 0.6018 (mtt) REVERT: N 39 GLN cc_start: 0.5817 (mp10) cc_final: 0.3977 (mp10) REVERT: L 32 SER cc_start: 0.8331 (t) cc_final: 0.7860 (p) REVERT: L 36 TRP cc_start: 0.8245 (m100) cc_final: 0.7900 (m100) REVERT: L 43 LYS cc_start: 0.8704 (mttt) cc_final: 0.8423 (mtpp) REVERT: L 48 LEU cc_start: 0.7934 (tp) cc_final: 0.7487 (tp) REVERT: L 74 LEU cc_start: 0.8161 (tt) cc_final: 0.7954 (tp) REVERT: L 87 TYR cc_start: 0.8563 (m-80) cc_final: 0.8022 (m-10) REVERT: L 91 GLN cc_start: 0.7811 (pp30) cc_final: 0.7569 (pp30) REVERT: L 166 THR cc_start: 0.8587 (t) cc_final: 0.8176 (m) outliers start: 22 outliers final: 18 residues processed: 214 average time/residue: 0.2636 time to fit residues: 78.5126 Evaluate side-chains 216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 A residue 64 VAL 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 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 Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 LEU 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: 0.6980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 93 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 51 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN L 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.167101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.148703 restraints weight = 13098.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.152417 restraints weight = 7163.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.154886 restraints weight = 4481.921| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8445 Z= 0.136 Angle : 0.603 9.983 11494 Z= 0.299 Chirality : 0.041 0.136 1296 Planarity : 0.005 0.093 1437 Dihedral : 4.999 53.928 1163 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.13 % Allowed : 16.80 % Favored : 81.08 % 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: 0.61 (0.27), residues: 386 sheet: -0.99 (0.32), residues: 243 loop : -1.94 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A -76 HIS 0.004 0.001 HIS A 355 PHE 0.011 0.001 PHE H 180 TYR 0.021 0.002 TYR A 149 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 420) hydrogen bonds : angle 4.98343 ( 1248) SS BOND : bond 0.00467 ( 5) SS BOND : angle 1.09162 ( 10) covalent geometry : bond 0.00299 ( 8440) covalent geometry : angle 0.60267 (11484) *********************** 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 215 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8249 (tttt) cc_final: 0.8038 (ttpt) REVERT: A -51 LYS cc_start: 0.7588 (tttt) cc_final: 0.7286 (mtmm) REVERT: A -50 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6309 (tmm) REVERT: A -49 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7490 (ttm170) REVERT: A 28 LEU cc_start: 0.7897 (mm) cc_final: 0.7536 (mp) REVERT: A 68 ILE cc_start: 0.6995 (mt) cc_final: 0.6748 (mm) REVERT: A 71 VAL cc_start: 0.7472 (m) cc_final: 0.7183 (p) REVERT: A 73 SER cc_start: 0.7925 (m) cc_final: 0.7466 (t) REVERT: A 99 GLN cc_start: 0.7647 (tt0) cc_final: 0.7322 (tt0) REVERT: A 294 GLU cc_start: 0.6858 (tt0) cc_final: 0.6569 (tt0) REVERT: A 386 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7088 (tp40) REVERT: H 20 SER cc_start: 0.8089 (m) cc_final: 0.7743 (p) REVERT: H 46 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8147 (mmmm) REVERT: H 135 VAL cc_start: 0.7926 (t) cc_final: 0.7604 (m) REVERT: H 136 PHE cc_start: 0.7650 (m-80) cc_final: 0.7434 (m-80) REVERT: N 34 MET cc_start: 0.6133 (mtt) cc_final: 0.5915 (mtt) REVERT: N 95 TYR cc_start: 0.6038 (m-10) cc_final: 0.5753 (m-10) REVERT: L 32 SER cc_start: 0.8190 (t) cc_final: 0.7710 (p) REVERT: L 36 TRP cc_start: 0.8135 (m100) cc_final: 0.7750 (m100) REVERT: L 37 TYR cc_start: 0.8311 (m-80) cc_final: 0.7547 (m-80) REVERT: L 43 LYS cc_start: 0.8701 (mttt) cc_final: 0.8406 (mtpp) REVERT: L 47 LEU cc_start: 0.8540 (tp) cc_final: 0.8272 (tt) REVERT: L 48 LEU cc_start: 0.7945 (tp) cc_final: 0.7504 (tp) REVERT: L 74 LEU cc_start: 0.8212 (tt) cc_final: 0.7977 (tp) REVERT: L 87 TYR cc_start: 0.8470 (m-80) cc_final: 0.7876 (m-10) REVERT: L 90 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: L 92 TYR cc_start: 0.8241 (p90) cc_final: 0.7434 (p90) outliers start: 19 outliers final: 13 residues processed: 205 average time/residue: 0.1975 time to fit residues: 56.0270 Evaluate side-chains 203 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 434 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 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 90 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 29 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 L 90 GLN L 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145427 restraints weight = 13161.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149281 restraints weight = 7098.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151811 restraints weight = 4403.237| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8445 Z= 0.166 Angle : 0.623 10.882 11494 Z= 0.312 Chirality : 0.042 0.148 1296 Planarity : 0.004 0.066 1437 Dihedral : 4.946 48.560 1163 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.46 % Allowed : 17.47 % Favored : 80.07 % 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: -1.11 (0.26), residues: 1045 helix: 0.60 (0.26), residues: 386 sheet: -0.88 (0.32), residues: 241 loop : -1.88 (0.30), residues: 418 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 0.015 0.001 PHE A 103 TYR 0.028 0.002 TYR A 149 ARG 0.008 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 420) hydrogen bonds : angle 5.01869 ( 1248) SS BOND : bond 0.00500 ( 5) SS BOND : angle 1.13220 ( 10) covalent geometry : bond 0.00359 ( 8440) covalent geometry : angle 0.62255 (11484) *********************** 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 217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8304 (tttt) cc_final: 0.8025 (ttpt) REVERT: A -51 LYS cc_start: 0.7681 (tttt) cc_final: 0.7360 (mtmm) REVERT: A -50 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6434 (tmm) REVERT: A -11 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 28 LEU cc_start: 0.7948 (mm) cc_final: 0.7354 (mp) REVERT: A 42 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7536 (mtm-85) REVERT: A 71 VAL cc_start: 0.7591 (m) cc_final: 0.7311 (p) REVERT: A 73 SER cc_start: 0.8064 (m) cc_final: 0.7649 (t) REVERT: A 99 GLN cc_start: 0.7739 (tt0) cc_final: 0.7283 (tt0) REVERT: A 122 MET cc_start: 0.7205 (tmm) cc_final: 0.5812 (tmm) REVERT: A 150 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7956 (mm-40) REVERT: A 264 ARG cc_start: 0.4525 (mtp85) cc_final: 0.4230 (mtm110) REVERT: A 373 ARG cc_start: 0.6645 (mmm-85) cc_final: 0.5633 (mmm-85) REVERT: A 386 GLN cc_start: 0.7410 (mm-40) cc_final: 0.6974 (tp40) REVERT: A 387 ILE cc_start: 0.7222 (mt) cc_final: 0.6889 (tp) REVERT: H 20 SER cc_start: 0.8072 (m) cc_final: 0.7732 (p) REVERT: H 46 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8138 (mmmm) REVERT: H 63 TYR cc_start: 0.7734 (m-10) cc_final: 0.7421 (m-10) REVERT: H 135 VAL cc_start: 0.7968 (t) cc_final: 0.7658 (m) REVERT: H 168 TRP cc_start: 0.7130 (m100) cc_final: 0.6793 (m100) REVERT: N 34 MET cc_start: 0.6210 (mtt) cc_final: 0.5968 (mtt) REVERT: N 95 TYR cc_start: 0.5975 (m-10) cc_final: 0.5686 (m-10) REVERT: L 32 SER cc_start: 0.8180 (t) cc_final: 0.7730 (p) REVERT: L 37 TYR cc_start: 0.8307 (m-80) cc_final: 0.7868 (m-80) REVERT: L 43 LYS cc_start: 0.8733 (mttt) cc_final: 0.8398 (mtpp) REVERT: L 74 LEU cc_start: 0.8206 (tt) cc_final: 0.7975 (tp) REVERT: L 87 TYR cc_start: 0.8457 (m-80) cc_final: 0.7871 (m-10) REVERT: L 92 TYR cc_start: 0.8230 (p90) cc_final: 0.7574 (p90) REVERT: L 166 THR cc_start: 0.8560 (t) cc_final: 0.8129 (m) outliers start: 22 outliers final: 14 residues processed: 206 average time/residue: 0.1891 time to fit residues: 53.7745 Evaluate side-chains 216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 -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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 28 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN 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 = 0.4023 r_free = 0.4023 target = 0.158904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140056 restraints weight = 13229.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.143709 restraints weight = 7201.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146219 restraints weight = 4519.918| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8445 Z= 0.198 Angle : 0.652 8.428 11494 Z= 0.327 Chirality : 0.042 0.159 1296 Planarity : 0.005 0.066 1437 Dihedral : 5.004 40.240 1163 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.69 % Allowed : 17.81 % Favored : 79.51 % 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: -1.15 (0.26), residues: 1045 helix: 0.47 (0.26), residues: 389 sheet: -0.86 (0.33), residues: 237 loop : -1.85 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 117 HIS 0.004 0.001 HIS A 355 PHE 0.026 0.001 PHE H 136 TYR 0.025 0.002 TYR H 53 ARG 0.008 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 420) hydrogen bonds : angle 5.17976 ( 1248) SS BOND : bond 0.00235 ( 5) SS BOND : angle 1.17293 ( 10) covalent geometry : bond 0.00429 ( 8440) covalent geometry : angle 0.65120 (11484) *********************** 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 230 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8400 (tttt) cc_final: 0.8180 (ttpt) REVERT: A -51 LYS cc_start: 0.7739 (tttt) cc_final: 0.7390 (mtmm) REVERT: A -50 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6204 (tmm) REVERT: A 71 VAL cc_start: 0.7587 (m) cc_final: 0.7218 (p) REVERT: A 73 SER cc_start: 0.8040 (m) cc_final: 0.7684 (t) REVERT: A 99 GLN cc_start: 0.7723 (tt0) cc_final: 0.7184 (tt0) REVERT: A 281 TYR cc_start: 0.6829 (t80) cc_final: 0.6507 (t80) REVERT: A 294 GLU cc_start: 0.6823 (tt0) cc_final: 0.6552 (tt0) REVERT: A 300 ASN cc_start: 0.6032 (t0) cc_final: 0.5821 (t0) REVERT: A 373 ARG cc_start: 0.6715 (mmm-85) cc_final: 0.6008 (ttm-80) REVERT: A 386 GLN cc_start: 0.7401 (mm-40) cc_final: 0.6977 (tp40) REVERT: A 387 ILE cc_start: 0.7207 (mt) cc_final: 0.6916 (tp) REVERT: A 440 LEU cc_start: 0.5767 (tp) cc_final: 0.5558 (tt) REVERT: H 37 LEU cc_start: 0.7961 (mm) cc_final: 0.7670 (mt) REVERT: H 46 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8117 (mmmm) REVERT: H 63 TYR cc_start: 0.7765 (m-10) cc_final: 0.7477 (m-10) REVERT: H 155 LEU cc_start: 0.7674 (tp) cc_final: 0.7460 (tt) REVERT: N 34 MET cc_start: 0.6272 (mtt) cc_final: 0.6051 (mtt) REVERT: N 83 MET cc_start: 0.6465 (ptm) cc_final: 0.6122 (ppp) REVERT: N 95 TYR cc_start: 0.6013 (m-10) cc_final: 0.5783 (m-10) REVERT: L 32 SER cc_start: 0.8271 (t) cc_final: 0.7898 (p) REVERT: L 36 TRP cc_start: 0.8261 (m100) cc_final: 0.7952 (m100) REVERT: L 43 LYS cc_start: 0.8733 (mttt) cc_final: 0.8432 (mtpp) REVERT: L 92 TYR cc_start: 0.8351 (p90) cc_final: 0.7986 (p90) REVERT: L 142 TYR cc_start: 0.7564 (t80) cc_final: 0.7050 (t80) REVERT: L 166 THR cc_start: 0.8598 (t) cc_final: 0.8183 (m) outliers start: 24 outliers final: 16 residues processed: 217 average time/residue: 0.2442 time to fit residues: 73.0777 Evaluate side-chains 217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET 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 26 ARG 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 L residue 16 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 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: 0.9980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN 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 = 0.4067 r_free = 0.4067 target = 0.162115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.143304 restraints weight = 13391.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.147058 restraints weight = 7274.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149558 restraints weight = 4518.689| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8445 Z= 0.155 Angle : 0.620 8.070 11494 Z= 0.310 Chirality : 0.041 0.178 1296 Planarity : 0.005 0.063 1437 Dihedral : 4.897 41.337 1163 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.02 % Allowed : 18.59 % Favored : 79.40 % 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: 0.66 (0.26), residues: 390 sheet: -0.90 (0.32), residues: 245 loop : -1.74 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.026 0.001 PHE H 136 TYR 0.026 0.002 TYR H 53 ARG 0.004 0.000 ARG N 52 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 420) hydrogen bonds : angle 4.96938 ( 1248) SS BOND : bond 0.00245 ( 5) SS BOND : angle 0.99549 ( 10) covalent geometry : bond 0.00343 ( 8440) covalent geometry : angle 0.61983 (11484) *********************** 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: 18 poor density : 204 time to evaluate : 0.906 Fit side-chains REVERT: A -56 LYS cc_start: 0.8379 (tttt) cc_final: 0.8164 (ttpt) REVERT: A -51 LYS cc_start: 0.7669 (tttt) cc_final: 0.7331 (mtmm) REVERT: A -50 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.5966 (tmm) REVERT: A 71 VAL cc_start: 0.7490 (m) cc_final: 0.7163 (p) REVERT: A 73 SER cc_start: 0.8189 (m) cc_final: 0.7782 (t) REVERT: A 99 GLN cc_start: 0.7679 (tt0) cc_final: 0.7120 (tt0) REVERT: A 122 MET cc_start: 0.7284 (tmm) cc_final: 0.6218 (tmm) REVERT: A 300 ASN cc_start: 0.6045 (t0) cc_final: 0.5828 (t0) REVERT: A 366 TYR cc_start: 0.6907 (m-80) cc_final: 0.6461 (m-80) REVERT: A 373 ARG cc_start: 0.6692 (mmm-85) cc_final: 0.5750 (mmm-85) REVERT: A 386 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6905 (tp40) REVERT: A 387 ILE cc_start: 0.7223 (mt) cc_final: 0.6908 (tp) REVERT: A 440 LEU cc_start: 0.5761 (tp) cc_final: 0.5545 (tt) REVERT: H 37 LEU cc_start: 0.7933 (mm) cc_final: 0.7630 (mt) REVERT: H 46 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8128 (mmmm) REVERT: H 63 TYR cc_start: 0.7745 (m-10) cc_final: 0.7526 (m-10) REVERT: H 168 TRP cc_start: 0.7121 (m100) cc_final: 0.6737 (m100) REVERT: H 206 GLN cc_start: 0.6948 (tt0) cc_final: 0.6631 (tt0) REVERT: N 34 MET cc_start: 0.6216 (mtt) cc_final: 0.5984 (mtt) REVERT: N 83 MET cc_start: 0.6670 (ptm) cc_final: 0.6157 (ppp) REVERT: L 5 MET cc_start: 0.7773 (tmm) cc_final: 0.7423 (ttp) REVERT: L 32 SER cc_start: 0.8217 (t) cc_final: 0.7940 (p) REVERT: L 36 TRP cc_start: 0.8183 (m100) cc_final: 0.7962 (m100) REVERT: L 48 LEU cc_start: 0.7909 (tp) cc_final: 0.7457 (tp) REVERT: L 87 TYR cc_start: 0.8460 (m-80) cc_final: 0.7921 (m-10) REVERT: L 92 TYR cc_start: 0.8345 (p90) cc_final: 0.7755 (p90) REVERT: L 142 TYR cc_start: 0.7516 (t80) cc_final: 0.6993 (t80) outliers start: 18 outliers final: 15 residues processed: 214 average time/residue: 0.2251 time to fit residues: 66.5522 Evaluate side-chains 213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 A residue 128 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 L residue 16 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 93 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4065 r_free = 0.4065 target = 0.162092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.143369 restraints weight = 13491.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.147160 restraints weight = 7331.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.149626 restraints weight = 4553.812| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8445 Z= 0.149 Angle : 0.637 9.298 11494 Z= 0.315 Chirality : 0.041 0.180 1296 Planarity : 0.005 0.063 1437 Dihedral : 4.848 36.474 1163 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.35 % Allowed : 18.92 % Favored : 78.72 % 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: -0.87 (0.26), residues: 1045 helix: 0.75 (0.26), residues: 390 sheet: -0.88 (0.32), residues: 246 loop : -1.62 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 107 HIS 0.004 0.001 HIS A 355 PHE 0.024 0.001 PHE H 136 TYR 0.027 0.002 TYR H 53 ARG 0.005 0.000 ARG A -21 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 420) hydrogen bonds : angle 4.88351 ( 1248) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.98040 ( 10) covalent geometry : bond 0.00329 ( 8440) covalent geometry : angle 0.63614 (11484) *********************** 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 222 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.942 Fit side-chains REVERT: A -56 LYS cc_start: 0.8323 (tttt) cc_final: 0.8109 (ttpt) REVERT: A -51 LYS cc_start: 0.7662 (tttt) cc_final: 0.7321 (mtmm) REVERT: A -50 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5898 (tmm) REVERT: A 73 SER cc_start: 0.7946 (m) cc_final: 0.7617 (t) REVERT: A 99 GLN cc_start: 0.7677 (tt0) cc_final: 0.7092 (tt0) REVERT: A 122 MET cc_start: 0.7484 (tmm) cc_final: 0.6227 (tmm) REVERT: A 366 TYR cc_start: 0.6918 (m-80) cc_final: 0.6625 (m-80) REVERT: A 386 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6910 (tp40) REVERT: A 387 ILE cc_start: 0.7201 (mt) cc_final: 0.6884 (tp) REVERT: A 440 LEU cc_start: 0.5757 (tp) cc_final: 0.5549 (tt) REVERT: H 20 SER cc_start: 0.8088 (m) cc_final: 0.7725 (p) REVERT: H 37 LEU cc_start: 0.7929 (mm) cc_final: 0.7623 (mt) REVERT: H 46 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8129 (mmmm) REVERT: N 34 MET cc_start: 0.6218 (mtt) cc_final: 0.6008 (mtt) REVERT: L 32 SER cc_start: 0.8245 (t) cc_final: 0.7905 (p) REVERT: L 36 TRP cc_start: 0.8208 (m100) cc_final: 0.8003 (m100) REVERT: L 48 LEU cc_start: 0.7970 (tp) cc_final: 0.7661 (tp) REVERT: L 90 GLN cc_start: 0.8108 (pt0) cc_final: 0.7369 (pt0) REVERT: L 92 TYR cc_start: 0.8314 (p90) cc_final: 0.7770 (p90) REVERT: L 142 TYR cc_start: 0.7530 (t80) cc_final: 0.7016 (t80) outliers start: 21 outliers final: 16 residues processed: 210 average time/residue: 0.2060 time to fit residues: 59.2208 Evaluate side-chains 214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 16 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 95 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 59 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4094 r_free = 0.4094 target = 0.164309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145558 restraints weight = 13359.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.149265 restraints weight = 7311.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.151815 restraints weight = 4610.864| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8445 Z= 0.133 Angle : 0.654 13.101 11494 Z= 0.317 Chirality : 0.041 0.170 1296 Planarity : 0.004 0.061 1437 Dihedral : 4.733 33.884 1163 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.90 % Allowed : 19.93 % Favored : 78.16 % 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: -0.72 (0.26), residues: 1045 helix: 0.93 (0.27), residues: 390 sheet: -0.71 (0.32), residues: 249 loop : -1.67 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.005 0.001 HIS A 118 PHE 0.025 0.001 PHE H 136 TYR 0.027 0.002 TYR H 53 ARG 0.011 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 420) hydrogen bonds : angle 4.77742 ( 1248) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.91619 ( 10) covalent geometry : bond 0.00293 ( 8440) covalent geometry : angle 0.65422 (11484) ********************** 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 218 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7543 (tttt) cc_final: 0.7209 (mtmm) REVERT: A -50 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.5871 (tmm) REVERT: A 73 SER cc_start: 0.7747 (m) cc_final: 0.7418 (t) REVERT: A 99 GLN cc_start: 0.7714 (tt0) cc_final: 0.7125 (tt0) REVERT: A 373 ARG cc_start: 0.6733 (mmm-85) cc_final: 0.5611 (tpp80) REVERT: A 387 ILE cc_start: 0.7197 (mt) cc_final: 0.6865 (tp) REVERT: H 20 SER cc_start: 0.8036 (m) cc_final: 0.7632 (p) REVERT: H 37 LEU cc_start: 0.7921 (mm) cc_final: 0.7617 (mt) REVERT: H 46 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8136 (mmmm) REVERT: H 168 TRP cc_start: 0.7233 (m100) cc_final: 0.6850 (m100) REVERT: H 198 VAL cc_start: 0.8639 (p) cc_final: 0.8413 (m) REVERT: N 34 MET cc_start: 0.6217 (mtt) cc_final: 0.6007 (mtt) REVERT: L 32 SER cc_start: 0.8170 (t) cc_final: 0.7807 (p) REVERT: L 36 TRP cc_start: 0.8204 (m100) cc_final: 0.7992 (m100) REVERT: L 48 LEU cc_start: 0.7996 (tp) cc_final: 0.7677 (tp) REVERT: L 74 LEU cc_start: 0.8117 (tt) cc_final: 0.7803 (tp) REVERT: L 90 GLN cc_start: 0.8103 (pt0) cc_final: 0.7527 (pt0) REVERT: L 92 TYR cc_start: 0.8264 (p90) cc_final: 0.7669 (p90) REVERT: L 142 TYR cc_start: 0.7520 (t80) cc_final: 0.6975 (t80) outliers start: 17 outliers final: 13 residues processed: 209 average time/residue: 0.2485 time to fit residues: 72.6716 Evaluate side-chains 213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 L residue 16 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.0060 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 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 = 0.4071 r_free = 0.4071 target = 0.162468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143694 restraints weight = 13477.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.147532 restraints weight = 7330.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150066 restraints weight = 4556.614| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8445 Z= 0.173 Angle : 0.673 9.866 11494 Z= 0.330 Chirality : 0.043 0.165 1296 Planarity : 0.005 0.062 1437 Dihedral : 4.874 29.335 1163 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.58 % Allowed : 19.82 % Favored : 77.60 % 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: -0.79 (0.26), residues: 1045 helix: 0.79 (0.26), residues: 390 sheet: -0.72 (0.32), residues: 250 loop : -1.64 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.025 0.002 PHE H 136 TYR 0.042 0.002 TYR A 149 ARG 0.004 0.000 ARG N 52 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 420) hydrogen bonds : angle 4.99707 ( 1248) SS BOND : bond 0.00242 ( 5) SS BOND : angle 0.99086 ( 10) covalent geometry : bond 0.00376 ( 8440) covalent geometry : angle 0.67294 (11484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3299.71 seconds wall clock time: 60 minutes 24.82 seconds (3624.82 seconds total)