Starting phenix.real_space_refine on Sat Aug 23 16:05:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2u_27846/08_2025/8e2u_27846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2u_27846/08_2025/8e2u_27846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e2u_27846/08_2025/8e2u_27846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2u_27846/08_2025/8e2u_27846.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2u_27846/08_2025/8e2u_27846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2u_27846/08_2025/8e2u_27846.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.089 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 S 35 5.16 5 C 4164 2.51 5 N 1144 2.21 5 O 1304 1.98 5 H 6581 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13228 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6728 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 15, 'TRANS': 423} Chain: "L" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3159 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "H" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3341 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Time building chain proxies: 2.37, per 1000 atoms: 0.18 Number of scatterers: 13228 At special positions: 0 Unit cell: (74.37, 117.66, 142.08, 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 35 16.00 O 1304 8.00 N 1144 7.00 C 4164 6.00 H 6581 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=1.62 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 212 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 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: 0.91 Conformation dependent library (CDL) restraints added in 408.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 15.6% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.602A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.560A pdb=" N GLY A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.790A pdb=" N THR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.558A pdb=" N LEU A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.590A pdb=" N CYS A 350 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 351 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.588A pdb=" N ALA L 128 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN L 129 " --> pdb=" O LEU L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.585A pdb=" N HIS L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.646A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.928A pdb=" N GLY A 42 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLY A 277 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG A 40 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 320 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.115A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.544A pdb=" N ALA A 159 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 269 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 267 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.511A pdb=" N MET A 372 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.925A pdb=" N LYS A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.721A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.715A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.150A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR L 173 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.231A pdb=" N TRP L 149 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR L 146 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 192 through 193 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.903A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.793A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AB6, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.537A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 181 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 150 through 153 removed outlier: 3.586A pdb=" N THR H 151 " --> pdb=" O ASN H 199 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 209 " --> pdb=" O CYS H 196 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 534 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: 2.63 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6581 1.04 - 1.24: 909 1.24 - 1.44: 1968 1.44 - 1.64: 3857 1.64 - 1.84: 44 Bond restraints: 13359 Sorted by residual: bond pdb=" C ASN H 82A" pdb=" O ASN H 82A" ideal model delta sigma weight residual 1.234 1.135 0.098 1.22e-02 6.72e+03 6.50e+01 bond pdb=" C ILE H 100 " pdb=" O ILE H 100 " ideal model delta sigma weight residual 1.235 1.145 0.090 1.31e-02 5.83e+03 4.70e+01 bond pdb=" N PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 1.473 1.406 0.067 1.40e-02 5.10e+03 2.29e+01 bond pdb=" C PRO H 147 " pdb=" O PRO H 147 " ideal model delta sigma weight residual 1.232 1.178 0.054 1.25e-02 6.40e+03 1.89e+01 bond pdb=" C GLN L 89 " pdb=" O GLN L 89 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.28e-02 6.10e+03 1.71e+01 ... (remaining 13354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 23698 3.12 - 6.24: 419 6.24 - 9.36: 24 9.36 - 12.48: 7 12.48 - 15.60: 1 Bond angle restraints: 24149 Sorted by residual: angle pdb=" CA ILE H 100 " pdb=" C ILE H 100 " pdb=" N SER H 100A" ideal model delta sigma weight residual 117.15 124.12 -6.97 7.80e-01 1.64e+00 7.98e+01 angle pdb=" CA ILE H 100 " pdb=" C ILE H 100 " pdb=" O ILE H 100 " ideal model delta sigma weight residual 120.80 113.33 7.47 8.90e-01 1.26e+00 7.04e+01 angle pdb=" N SER A 293 " pdb=" CA SER A 293 " pdb=" C SER A 293 " ideal model delta sigma weight residual 107.62 92.02 15.60 1.97e+00 2.58e-01 6.27e+01 angle pdb=" CA PRO H 147 " pdb=" C PRO H 147 " pdb=" O PRO H 147 " ideal model delta sigma weight residual 121.96 112.91 9.05 1.23e+00 6.61e-01 5.41e+01 angle pdb=" CA PRO H 147 " pdb=" C PRO H 147 " pdb=" N GLU H 148 " ideal model delta sigma weight residual 114.74 122.32 -7.58 1.03e+00 9.43e-01 5.41e+01 ... (remaining 24144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5716 17.72 - 35.43: 426 35.43 - 53.15: 173 53.15 - 70.86: 47 70.86 - 88.58: 13 Dihedral angle restraints: 6375 sinusoidal: 3489 harmonic: 2886 Sorted by residual: dihedral pdb=" CB CYS A 292 " pdb=" SG CYS A 292 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 39.54 53.46 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS L 212 " pdb=" SG CYS L 212 " pdb=" SG CYS H 216 " pdb=" CB CYS H 216 " ideal model delta sinusoidal sigma weight residual 93.00 140.90 -47.90 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 135.96 -42.96 1 1.00e+01 1.00e-02 2.57e+01 ... (remaining 6372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 754 0.049 - 0.098: 224 0.098 - 0.148: 66 0.148 - 0.197: 14 0.197 - 0.246: 2 Chirality restraints: 1060 Sorted by residual: chirality pdb=" CA GLN L 168 " pdb=" N GLN L 168 " pdb=" C GLN L 168 " pdb=" CB GLN L 168 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASP L 152 " pdb=" N ASP L 152 " pdb=" C ASP L 152 " pdb=" CB ASP L 152 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE H 146 " pdb=" N PHE H 146 " pdb=" C PHE H 146 " pdb=" CB PHE H 146 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1057 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 82A" 0.035 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CG ASN H 82A" 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN H 82A" -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN H 82A" -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN H 82A" -0.745 2.00e-02 2.50e+03 pdb="HD22 ASN H 82A" 0.739 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 168 " 0.164 2.00e-02 2.50e+03 4.10e-01 2.52e+03 pdb=" CD GLN L 168 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN L 168 " -0.159 2.00e-02 2.50e+03 pdb=" NE2 GLN L 168 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN L 168 " -0.686 2.00e-02 2.50e+03 pdb="HE22 GLN L 168 " 0.695 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 455 " 0.165 2.00e-02 2.50e+03 4.10e-01 2.52e+03 pdb=" CD GLN A 455 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A 455 " -0.157 2.00e-02 2.50e+03 pdb=" NE2 GLN A 455 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 455 " 0.697 2.00e-02 2.50e+03 pdb="HE22 GLN A 455 " -0.684 2.00e-02 2.50e+03 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 180 2.02 - 2.67: 18621 2.67 - 3.31: 35296 3.31 - 3.96: 45513 3.96 - 4.60: 70091 Nonbonded interactions: 169701 Sorted by model distance: nonbonded pdb=" OE2 GLU A 21 " pdb=" HG SER A 376 " model vdw 1.380 2.450 nonbonded pdb=" HG1 THR L 146 " pdb=" HG1 THR L 197 " model vdw 1.436 2.100 nonbonded pdb=" O CYS A 60 " pdb=" HZ3 LYS A 68 " model vdw 1.437 2.450 nonbonded pdb=" HH TYR A 23 " pdb=" O CYS A 407 " model vdw 1.526 2.450 nonbonded pdb=" OE1 GLU A 21 " pdb=" HH TYR A 409 " model vdw 1.542 2.450 ... (remaining 169696 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.060 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.420 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.007 0.407 6791 Z= 0.419 Angle : 1.072 42.976 9238 Z= 0.651 Chirality : 0.052 0.246 1060 Planarity : 0.007 0.112 1186 Dihedral : 14.007 88.580 2459 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.24 % Favored : 91.42 % Rotamer: Outliers : 0.94 % Allowed : 1.08 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.28), residues: 874 helix: -1.75 (0.43), residues: 137 sheet: 0.12 (0.36), residues: 258 loop : -2.21 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 175 TYR 0.037 0.002 TYR A 299 PHE 0.019 0.002 PHE A 446 TRP 0.016 0.002 TRP H 100D HIS 0.006 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 6778) covalent geometry : angle 0.97100 ( 9212) SS BOND : bond 0.11289 ( 13) SS BOND : angle 8.61027 ( 26) hydrogen bonds : bond 0.26623 ( 206) hydrogen bonds : angle 9.31625 ( 534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7441 (tp30) cc_final: 0.7075 (tp30) REVERT: A 346 GLN cc_start: 0.7167 (pt0) cc_final: 0.6929 (pt0) REVERT: L 132 THR cc_start: 0.8440 (p) cc_final: 0.8063 (p) REVERT: H 195 ILE cc_start: 0.7649 (mp) cc_final: 0.7396 (pt) outliers start: 7 outliers final: 1 residues processed: 81 average time/residue: 0.1173 time to fit residues: 14.3577 Evaluate side-chains 61 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 413 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.215458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.172299 restraints weight = 21955.668| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.22 r_work: 0.4071 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6791 Z= 0.145 Angle : 0.631 5.617 9238 Z= 0.336 Chirality : 0.047 0.161 1060 Planarity : 0.005 0.054 1186 Dihedral : 5.460 60.722 950 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 0.54 % Allowed : 7.14 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.28), residues: 874 helix: -1.07 (0.46), residues: 131 sheet: 0.37 (0.35), residues: 268 loop : -2.31 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.015 0.001 TYR L 49 PHE 0.012 0.001 PHE H 122 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6778) covalent geometry : angle 0.62792 ( 9212) SS BOND : bond 0.00449 ( 13) SS BOND : angle 1.33105 ( 26) hydrogen bonds : bond 0.05059 ( 206) hydrogen bonds : angle 6.68098 ( 534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7913 (tp30) cc_final: 0.7362 (tp30) REVERT: L 48 ILE cc_start: 0.8257 (mm) cc_final: 0.7898 (mt) REVERT: L 125 GLU cc_start: 0.6121 (tt0) cc_final: 0.5862 (tt0) REVERT: H 59 TYR cc_start: 0.8698 (m-80) cc_final: 0.8455 (m-80) REVERT: H 144 ASP cc_start: 0.7033 (m-30) cc_final: 0.6766 (m-30) REVERT: H 195 ILE cc_start: 0.8149 (mp) cc_final: 0.7896 (pt) outliers start: 4 outliers final: 4 residues processed: 67 average time/residue: 0.1103 time to fit residues: 10.9273 Evaluate side-chains 64 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 0.0040 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.213901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.173889 restraints weight = 22126.267| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 2.15 r_work: 0.4036 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6791 Z= 0.136 Angle : 0.574 5.246 9238 Z= 0.303 Chirality : 0.045 0.153 1060 Planarity : 0.004 0.048 1186 Dihedral : 4.837 19.565 947 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.44 % Favored : 92.45 % Rotamer: Outliers : 0.81 % Allowed : 9.03 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.28), residues: 874 helix: -0.73 (0.47), residues: 131 sheet: 0.26 (0.34), residues: 269 loop : -2.31 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 33 TYR 0.017 0.001 TYR A 359 PHE 0.011 0.001 PHE H 100E TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6778) covalent geometry : angle 0.57288 ( 9212) SS BOND : bond 0.00377 ( 13) SS BOND : angle 0.93005 ( 26) hydrogen bonds : bond 0.04368 ( 206) hydrogen bonds : angle 6.14356 ( 534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7586 (tt0) cc_final: 0.7274 (tt0) REVERT: A 25 GLU cc_start: 0.8016 (tp30) cc_final: 0.7522 (tp30) REVERT: H 195 ILE cc_start: 0.8182 (mp) cc_final: 0.7920 (pt) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.1210 time to fit residues: 11.8751 Evaluate side-chains 65 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.211987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.169223 restraints weight = 22016.113| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 2.34 r_work: 0.3987 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6791 Z= 0.152 Angle : 0.575 5.236 9238 Z= 0.303 Chirality : 0.046 0.166 1060 Planarity : 0.004 0.049 1186 Dihedral : 4.819 20.023 947 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.01 % Favored : 91.88 % Rotamer: Outliers : 0.67 % Allowed : 10.24 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.28), residues: 874 helix: -0.63 (0.48), residues: 132 sheet: 0.13 (0.32), residues: 290 loop : -2.42 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 33 TYR 0.016 0.001 TYR L 49 PHE 0.013 0.001 PHE H 100E TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6778) covalent geometry : angle 0.57367 ( 9212) SS BOND : bond 0.00327 ( 13) SS BOND : angle 0.87311 ( 26) hydrogen bonds : bond 0.03761 ( 206) hydrogen bonds : angle 5.79058 ( 534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7462 (tt0) cc_final: 0.7213 (tt0) REVERT: A 25 GLU cc_start: 0.7895 (tp30) cc_final: 0.7336 (tp30) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.1227 time to fit residues: 12.6478 Evaluate side-chains 66 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 47 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.241388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.194638 restraints weight = 22731.035| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 2.92 r_work: 0.3975 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6791 Z= 0.122 Angle : 0.546 5.196 9238 Z= 0.285 Chirality : 0.045 0.146 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.695 19.188 947 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.24 % Favored : 91.65 % Rotamer: Outliers : 1.35 % Allowed : 11.05 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.28), residues: 874 helix: -0.53 (0.49), residues: 132 sheet: 0.17 (0.33), residues: 279 loop : -2.34 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 33 TYR 0.013 0.001 TYR L 49 PHE 0.010 0.001 PHE H 100E TRP 0.010 0.001 TRP H 154 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6778) covalent geometry : angle 0.54563 ( 9212) SS BOND : bond 0.00293 ( 13) SS BOND : angle 0.70233 ( 26) hydrogen bonds : bond 0.03424 ( 206) hydrogen bonds : angle 5.51171 ( 534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8022 (tp30) cc_final: 0.7392 (tp30) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1486 time to fit residues: 16.3200 Evaluate side-chains 73 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.211313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.169147 restraints weight = 22059.631| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.07 r_work: 0.3897 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6791 Z= 0.142 Angle : 0.560 5.177 9238 Z= 0.293 Chirality : 0.045 0.160 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.681 19.375 947 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.70 % Favored : 91.19 % Rotamer: Outliers : 1.48 % Allowed : 11.46 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.28), residues: 874 helix: -0.47 (0.49), residues: 132 sheet: 0.08 (0.32), residues: 279 loop : -2.35 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 33 TYR 0.015 0.001 TYR A 359 PHE 0.013 0.001 PHE H 100E TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6778) covalent geometry : angle 0.55915 ( 9212) SS BOND : bond 0.00320 ( 13) SS BOND : angle 0.76670 ( 26) hydrogen bonds : bond 0.03393 ( 206) hydrogen bonds : angle 5.43825 ( 534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7819 (tp30) cc_final: 0.7296 (tp30) outliers start: 11 outliers final: 10 residues processed: 73 average time/residue: 0.1392 time to fit residues: 14.7431 Evaluate side-chains 74 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.238777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.199132 restraints weight = 22637.524| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.06 r_work: 0.3986 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6791 Z= 0.159 Angle : 0.565 5.214 9238 Z= 0.296 Chirality : 0.045 0.145 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.732 19.909 947 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.92 % Favored : 90.96 % Rotamer: Outliers : 1.48 % Allowed : 11.59 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.28), residues: 874 helix: -0.42 (0.49), residues: 131 sheet: -0.02 (0.32), residues: 277 loop : -2.37 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 33 TYR 0.018 0.001 TYR L 49 PHE 0.014 0.001 PHE H 100E TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6778) covalent geometry : angle 0.56415 ( 9212) SS BOND : bond 0.00339 ( 13) SS BOND : angle 0.78271 ( 26) hydrogen bonds : bond 0.03399 ( 206) hydrogen bonds : angle 5.44092 ( 534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7882 (tp30) cc_final: 0.7237 (tp30) REVERT: A 209 ASP cc_start: 0.7003 (t0) cc_final: 0.6615 (t0) REVERT: L 195 GLN cc_start: 0.7853 (tt0) cc_final: 0.7359 (tt0) outliers start: 11 outliers final: 11 residues processed: 73 average time/residue: 0.1526 time to fit residues: 15.6782 Evaluate side-chains 75 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN L 38 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.237480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.193342 restraints weight = 22641.178| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.39 r_work: 0.3857 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6791 Z= 0.167 Angle : 0.573 5.284 9238 Z= 0.301 Chirality : 0.045 0.146 1060 Planarity : 0.004 0.049 1186 Dihedral : 4.743 20.434 947 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.81 % Favored : 91.08 % Rotamer: Outliers : 1.75 % Allowed : 11.46 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.28), residues: 874 helix: -0.63 (0.46), residues: 141 sheet: -0.09 (0.32), residues: 277 loop : -2.41 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 33 TYR 0.018 0.001 TYR L 49 PHE 0.015 0.001 PHE H 100E TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6778) covalent geometry : angle 0.57277 ( 9212) SS BOND : bond 0.00347 ( 13) SS BOND : angle 0.78505 ( 26) hydrogen bonds : bond 0.03399 ( 206) hydrogen bonds : angle 5.43924 ( 534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7895 (tp30) cc_final: 0.7360 (tp30) REVERT: A 209 ASP cc_start: 0.7080 (t0) cc_final: 0.6666 (t0) REVERT: L 195 GLN cc_start: 0.7995 (tt0) cc_final: 0.7679 (tt0) outliers start: 13 outliers final: 13 residues processed: 76 average time/residue: 0.1273 time to fit residues: 14.3930 Evaluate side-chains 77 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 197 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 70 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.211317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.169512 restraints weight = 22159.906| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.26 r_work: 0.3967 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6791 Z= 0.121 Angle : 0.547 5.253 9238 Z= 0.285 Chirality : 0.044 0.147 1060 Planarity : 0.004 0.050 1186 Dihedral : 4.706 19.647 947 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.35 % Favored : 91.53 % Rotamer: Outliers : 1.75 % Allowed : 11.59 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.28), residues: 874 helix: -0.45 (0.47), residues: 137 sheet: -0.04 (0.33), residues: 277 loop : -2.32 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 33 TYR 0.012 0.001 TYR L 49 PHE 0.010 0.001 PHE H 100E TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6778) covalent geometry : angle 0.54696 ( 9212) SS BOND : bond 0.00313 ( 13) SS BOND : angle 0.67533 ( 26) hydrogen bonds : bond 0.03158 ( 206) hydrogen bonds : angle 5.32397 ( 534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7940 (tp30) cc_final: 0.7299 (tp30) REVERT: A 209 ASP cc_start: 0.7025 (t0) cc_final: 0.6617 (t0) outliers start: 13 outliers final: 12 residues processed: 74 average time/residue: 0.1362 time to fit residues: 14.3091 Evaluate side-chains 77 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 20 optimal weight: 0.0970 chunk 74 optimal weight: 0.0980 chunk 29 optimal weight: 0.0040 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.213533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.171057 restraints weight = 22091.504| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.40 r_work: 0.4017 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 6791 Z= 0.095 Angle : 0.522 5.350 9238 Z= 0.269 Chirality : 0.044 0.149 1060 Planarity : 0.004 0.048 1186 Dihedral : 4.470 18.054 947 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.55 % Favored : 92.33 % Rotamer: Outliers : 0.94 % Allowed : 12.40 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.28), residues: 874 helix: -0.33 (0.48), residues: 137 sheet: 0.04 (0.32), residues: 281 loop : -2.24 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 248 TYR 0.009 0.001 TYR A 359 PHE 0.006 0.001 PHE H 100E TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6778) covalent geometry : angle 0.52148 ( 9212) SS BOND : bond 0.00280 ( 13) SS BOND : angle 0.59677 ( 26) hydrogen bonds : bond 0.02815 ( 206) hydrogen bonds : angle 5.06451 ( 534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7949 (tp30) cc_final: 0.7331 (tp30) REVERT: A 209 ASP cc_start: 0.6972 (t0) cc_final: 0.6554 (t0) REVERT: H 59 TYR cc_start: 0.8558 (m-80) cc_final: 0.8084 (m-80) outliers start: 7 outliers final: 7 residues processed: 69 average time/residue: 0.1513 time to fit residues: 14.9763 Evaluate side-chains 72 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.211818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.169935 restraints weight = 22113.108| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.27 r_work: 0.3905 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6791 Z= 0.123 Angle : 0.535 5.241 9238 Z= 0.277 Chirality : 0.044 0.156 1060 Planarity : 0.004 0.048 1186 Dihedral : 4.483 18.293 947 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.47 % Favored : 91.42 % Rotamer: Outliers : 1.35 % Allowed : 11.99 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.28), residues: 874 helix: -0.33 (0.47), residues: 137 sheet: 0.04 (0.33), residues: 277 loop : -2.24 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 33 TYR 0.014 0.001 TYR L 49 PHE 0.011 0.001 PHE H 100E TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6778) covalent geometry : angle 0.53491 ( 9212) SS BOND : bond 0.00322 ( 13) SS BOND : angle 0.67378 ( 26) hydrogen bonds : bond 0.02943 ( 206) hydrogen bonds : angle 5.09299 ( 534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2854.75 seconds wall clock time: 49 minutes 4.11 seconds (2944.11 seconds total)