Starting phenix.real_space_refine on Tue Aug 4 19:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrd_37774/08_2026/8wrd_37774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrd_37774/08_2026/8wrd_37774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wrd_37774/08_2026/8wrd_37774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrd_37774/08_2026/8wrd_37774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wrd_37774/08_2026/8wrd_37774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrd_37774/08_2026/8wrd_37774.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4078 2.51 5 N 1017 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6326 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2957 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 23, 'TRANS': 369} Chain breaks: 1 Chain: "L" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "H" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1702 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Time building chain proxies: 1.61, per 1000 atoms: 0.25 Number of scatterers: 6326 At special positions: 0 Unit cell: (84.48, 84.48, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1189 8.00 N 1017 7.00 C 4078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 206 " distance=2.04 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: 0.38 Conformation dependent library (CDL) restraints added in 353.9 milliseconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 46.9% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 removed outlier: 3.733A pdb=" N TRP A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.807A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 157 removed outlier: 3.815A pdb=" N GLY A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.707A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 177 Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.731A pdb=" N ARG A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.549A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.714A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 4.295A pdb=" N ALA A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 324 removed outlier: 3.860A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.777A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.610A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.518A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 4.924A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 removed outlier: 3.939A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.975A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.522A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.548A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.847A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.767A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.514A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.808A 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 helix chain 'H' and resid 62 through 65 removed outlier: 3.676A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.583A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.589A pdb=" N SER H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.508A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.589A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 118 removed outlier: 3.862A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.593A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.693A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA H 110 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 131 through 135 removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.627A pdb=" N THR H 215 " --> pdb=" O HIS H 210 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1041 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: 1.26 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1957 1.34 - 1.46: 1540 1.46 - 1.58: 2914 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 6478 Sorted by residual: bond pdb=" CA LYS H 126 " pdb=" CB LYS H 126 " ideal model delta sigma weight residual 1.533 1.546 -0.013 1.37e-02 5.33e+03 8.60e-01 bond pdb=" C ILE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.31e-01 bond pdb=" CB ASP H 103 " pdb=" CG ASP H 103 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.12e-01 bond pdb=" CB LYS H 126 " pdb=" CG LYS H 126 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.86e-01 bond pdb=" CB VAL L 146 " pdb=" CG2 VAL L 146 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.53e-01 ... (remaining 6473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8657 1.61 - 3.23: 121 3.23 - 4.84: 28 4.84 - 6.45: 9 6.45 - 8.06: 1 Bond angle restraints: 8816 Sorted by residual: angle pdb=" CA LYS H 126 " pdb=" CB LYS H 126 " pdb=" CG LYS H 126 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 115.40 -5.59 2.21e+00 2.05e-01 6.41e+00 angle pdb=" N GLY A 436 " pdb=" CA GLY A 436 " pdb=" C GLY A 436 " ideal model delta sigma weight residual 112.34 117.07 -4.73 2.04e+00 2.40e-01 5.39e+00 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 110.70 113.28 -2.58 1.22e+00 6.72e-01 4.48e+00 angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.42 113.57 -3.15 1.49e+00 4.50e-01 4.47e+00 ... (remaining 8811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 3344 17.15 - 34.30: 374 34.30 - 51.45: 98 51.45 - 68.61: 18 68.61 - 85.76: 6 Dihedral angle restraints: 3840 sinusoidal: 1451 harmonic: 2389 Sorted by residual: dihedral pdb=" CA LYS H 126 " pdb=" C LYS H 126 " pdb=" N THR H 127 " pdb=" CA THR H 127 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LEU L 136 " pdb=" C LEU L 136 " pdb=" N ASN L 137 " pdb=" CA ASN L 137 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 58.97 34.03 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 3837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 604 0.029 - 0.058: 260 0.058 - 0.087: 87 0.087 - 0.116: 59 0.116 - 0.145: 8 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE L 144 " pdb=" N ILE L 144 " pdb=" C ILE L 144 " pdb=" CB ILE L 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1015 not shown) Planarity restraints: 1103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 126 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C LYS H 126 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS H 126 " -0.014 2.00e-02 2.50e+03 pdb=" N THR H 127 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 161 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 386 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 387 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.023 5.00e-02 4.00e+02 ... (remaining 1100 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 265 2.72 - 3.27: 6059 3.27 - 3.81: 10078 3.81 - 4.36: 12165 4.36 - 4.90: 22210 Nonbonded interactions: 50777 Sorted by model distance: nonbonded pdb=" O ASN L 137 " pdb=" OG SER L 174 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR H 195 " pdb=" OG1 THR H 198 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 291 " pdb=" NE2 HIS A 414 " model vdw 2.287 3.120 nonbonded pdb=" OD1 ASP A 291 " pdb=" NH1 ARG A 413 " model vdw 2.310 3.120 nonbonded pdb=" O GLU L 123 " pdb=" OG1 THR L 126 " model vdw 2.316 3.040 ... (remaining 50772 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.040 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:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.004 0.033 6482 Z= 0.146 Angle : 0.552 8.063 8824 Z= 0.285 Chirality : 0.042 0.145 1018 Planarity : 0.004 0.044 1103 Dihedral : 15.710 85.756 2300 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.14 % Allowed : 22.33 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.84 (0.30), residues: 822 helix: 1.34 (0.30), residues: 329 sheet: 1.38 (0.36), residues: 221 loop : -1.13 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 155 TYR 0.012 0.001 TYR A 422 PHE 0.012 0.001 PHE L 87 TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6478) covalent geometry : angle 0.55189 / 0.28 ( 8816) SS BOND : bond 0.00397 / 0.19 ( 4) SS BOND : angle 0.87427 / 0.52 ( 8) hydrogen bonds : bond 0.14359 / 10.03 ( 347) hydrogen bonds : angle 6.89795 / 5.18 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.260 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.1111 time to fit residues: 9.1635 Evaluate side-chains 61 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN L 210 ASN H 59 ASN H 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093338 restraints weight = 8189.394| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.19 r_work: 0.2979 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6482 Z= 0.187 Angle : 0.592 6.093 8824 Z= 0.309 Chirality : 0.043 0.135 1018 Planarity : 0.005 0.045 1103 Dihedral : 4.615 23.803 884 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 20.91 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.73 (0.30), residues: 822 helix: 1.14 (0.29), residues: 334 sheet: 1.25 (0.36), residues: 217 loop : -0.95 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.011 0.001 TYR L 140 PHE 0.013 0.001 PHE L 87 TRP 0.010 0.001 TRP H 114 HIS 0.002 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 ( 6478) covalent geometry : angle 0.59157 / 0.31 ( 8816) SS BOND : bond 0.00445 / 0.22 ( 4) SS BOND : angle 0.99101 / 0.60 ( 8) hydrogen bonds : bond 0.04732 / 3.16 ( 347) hydrogen bonds : angle 5.36366 / 3.98 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.295 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.0859 time to fit residues: 8.8576 Evaluate side-chains 70 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 195 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095195 restraints weight = 8160.564| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.14 r_work: 0.3014 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6482 Z= 0.132 Angle : 0.542 6.277 8824 Z= 0.281 Chirality : 0.041 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.493 24.504 884 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.99 % Allowed : 21.19 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.85 (0.30), residues: 822 helix: 1.33 (0.30), residues: 334 sheet: 1.21 (0.35), residues: 222 loop : -0.98 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 155 TYR 0.009 0.001 TYR L 140 PHE 0.011 0.001 PHE L 87 TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 6478) covalent geometry : angle 0.54113 / 0.28 ( 8816) SS BOND : bond 0.00405 / 0.20 ( 4) SS BOND : angle 1.23697 / 0.73 ( 8) hydrogen bonds : bond 0.03921 / 2.61 ( 347) hydrogen bonds : angle 4.99020 / 3.67 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.150 Fit side-chains REVERT: L 6 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: H 89 ASP cc_start: 0.8584 (t0) cc_final: 0.8243 (t0) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 0.0627 time to fit residues: 7.2852 Evaluate side-chains 76 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096009 restraints weight = 8168.098| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.18 r_work: 0.3022 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6482 Z= 0.124 Angle : 0.533 6.442 8824 Z= 0.274 Chirality : 0.041 0.138 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.403 24.281 884 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.27 % Allowed : 20.77 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.88 (0.30), residues: 822 helix: 1.41 (0.30), residues: 332 sheet: 1.20 (0.35), residues: 222 loop : -1.00 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.009 0.001 TYR L 49 PHE 0.011 0.001 PHE L 87 TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 6478) covalent geometry : angle 0.53244 / 0.27 ( 8816) SS BOND : bond 0.00486 / 0.24 ( 4) SS BOND : angle 1.11434 / 0.66 ( 8) hydrogen bonds : bond 0.03698 / 2.45 ( 347) hydrogen bonds : angle 4.79324 / 3.53 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.144 Fit side-chains REVERT: L 6 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: H 89 ASP cc_start: 0.8585 (t0) cc_final: 0.8259 (t0) outliers start: 30 outliers final: 20 residues processed: 96 average time/residue: 0.0663 time to fit residues: 8.6406 Evaluate side-chains 87 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 77 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.8958 > 50:) chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095402 restraints weight = 8280.215| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.22 r_work: 0.3005 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6482 Z= 0.136 Angle : 0.540 6.344 8824 Z= 0.278 Chirality : 0.042 0.136 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.423 23.578 884 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.84 % Allowed : 21.05 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.86 (0.30), residues: 822 helix: 1.38 (0.30), residues: 332 sheet: 1.18 (0.35), residues: 222 loop : -0.97 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.009 0.001 TYR L 140 PHE 0.011 0.001 PHE L 87 TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6478) covalent geometry : angle 0.53894 / 0.28 ( 8816) SS BOND : bond 0.00516 / 0.26 ( 4) SS BOND : angle 1.03114 / 0.62 ( 8) hydrogen bonds : bond 0.03874 / 2.56 ( 347) hydrogen bonds : angle 4.77970 / 3.52 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.179 Fit side-chains REVERT: L 6 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: H 89 ASP cc_start: 0.8629 (t0) cc_final: 0.8338 (t0) outliers start: 27 outliers final: 22 residues processed: 92 average time/residue: 0.0649 time to fit residues: 8.2735 Evaluate side-chains 89 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092473 restraints weight = 8245.835| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.21 r_work: 0.2963 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6482 Z= 0.201 Angle : 0.602 7.591 8824 Z= 0.310 Chirality : 0.044 0.136 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.696 24.823 884 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.41 % Allowed : 21.48 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.65 (0.30), residues: 822 helix: 1.14 (0.30), residues: 332 sheet: 1.10 (0.35), residues: 217 loop : -0.95 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.013 0.001 TYR L 140 PHE 0.013 0.001 PHE L 87 TRP 0.011 0.001 TRP H 114 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.20 ( 6478) covalent geometry : angle 0.60097 / 0.31 ( 8816) SS BOND : bond 0.00565 / 0.28 ( 4) SS BOND : angle 1.27098 / 0.77 ( 8) hydrogen bonds : bond 0.04739 / 3.13 ( 347) hydrogen bonds : angle 4.97026 / 3.66 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.148 Fit side-chains REVERT: A 185 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8455 (mp) REVERT: A 244 GLU cc_start: 0.7983 (pp20) cc_final: 0.7442 (tm-30) REVERT: L 6 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: H 89 ASP cc_start: 0.8656 (t0) cc_final: 0.8395 (t0) outliers start: 31 outliers final: 25 residues processed: 95 average time/residue: 0.0643 time to fit residues: 8.3961 Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094343 restraints weight = 8189.218| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.19 r_work: 0.2994 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6482 Z= 0.146 Angle : 0.557 7.207 8824 Z= 0.288 Chirality : 0.042 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.568 25.074 884 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.69 % Allowed : 20.77 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.75 (0.30), residues: 822 helix: 1.28 (0.30), residues: 331 sheet: 1.10 (0.34), residues: 222 loop : -0.99 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.010 0.001 TYR L 140 PHE 0.012 0.001 PHE L 87 TRP 0.010 0.001 TRP H 114 HIS 0.002 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 6478) covalent geometry : angle 0.55692 / 0.29 ( 8816) SS BOND : bond 0.00473 / 0.23 ( 4) SS BOND : angle 0.91319 / 0.56 ( 8) hydrogen bonds : bond 0.04062 / 2.69 ( 347) hydrogen bonds : angle 4.81787 / 3.55 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.243 Fit side-chains REVERT: A 244 GLU cc_start: 0.7993 (pp20) cc_final: 0.7350 (tm-30) REVERT: L 6 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: H 89 ASP cc_start: 0.8690 (t0) cc_final: 0.8420 (t0) outliers start: 33 outliers final: 28 residues processed: 99 average time/residue: 0.0630 time to fit residues: 8.7932 Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095779 restraints weight = 8211.877| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.20 r_work: 0.3014 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6482 Z= 0.125 Angle : 0.540 7.456 8824 Z= 0.279 Chirality : 0.041 0.134 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.443 24.059 884 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.27 % Allowed : 21.34 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.80 (0.30), residues: 822 helix: 1.39 (0.30), residues: 331 sheet: 1.09 (0.35), residues: 219 loop : -0.99 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.009 0.001 TYR L 49 PHE 0.011 0.001 PHE L 87 TRP 0.009 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 6478) covalent geometry : angle 0.53982 / 0.28 ( 8816) SS BOND : bond 0.00455 / 0.22 ( 4) SS BOND : angle 0.77789 / 0.48 ( 8) hydrogen bonds : bond 0.03721 / 2.46 ( 347) hydrogen bonds : angle 4.70273 / 3.47 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.171 Fit side-chains REVERT: A 244 GLU cc_start: 0.8005 (pp20) cc_final: 0.7466 (tm-30) REVERT: H 89 ASP cc_start: 0.8714 (t0) cc_final: 0.8444 (t0) outliers start: 30 outliers final: 25 residues processed: 96 average time/residue: 0.0618 time to fit residues: 8.1918 Evaluate side-chains 91 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 64 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 77 ASN H 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096769 restraints weight = 8306.705| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.21 r_work: 0.3029 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6482 Z= 0.117 Angle : 0.533 7.682 8824 Z= 0.275 Chirality : 0.041 0.137 1018 Planarity : 0.004 0.043 1103 Dihedral : 4.354 23.750 884 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.70 % Allowed : 21.62 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.87 (0.30), residues: 822 helix: 1.49 (0.30), residues: 331 sheet: 1.13 (0.35), residues: 215 loop : -0.99 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 211 TYR 0.009 0.001 TYR L 49 PHE 0.011 0.001 PHE L 87 TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6478) covalent geometry : angle 0.53305 / 0.27 ( 8816) SS BOND : bond 0.00462 / 0.23 ( 4) SS BOND : angle 0.73197 / 0.45 ( 8) hydrogen bonds : bond 0.03518 / 2.32 ( 347) hydrogen bonds : angle 4.61601 / 3.41 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.183 Fit side-chains REVERT: A 244 GLU cc_start: 0.7980 (pp20) cc_final: 0.7454 (tm-30) REVERT: L 211 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7111 (mtm110) REVERT: H 84 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7857 (p) REVERT: H 89 ASP cc_start: 0.8710 (t0) cc_final: 0.8460 (t0) outliers start: 26 outliers final: 24 residues processed: 91 average time/residue: 0.0713 time to fit residues: 8.8929 Evaluate side-chains 90 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.095137 restraints weight = 8198.723| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.19 r_work: 0.3004 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6482 Z= 0.145 Angle : 0.558 6.631 8824 Z= 0.287 Chirality : 0.042 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.423 22.934 884 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.70 % Allowed : 21.62 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.81 (0.30), residues: 822 helix: 1.33 (0.30), residues: 337 sheet: 1.11 (0.35), residues: 215 loop : -0.94 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.010 0.001 TYR L 140 PHE 0.011 0.001 PHE L 87 TRP 0.010 0.001 TRP H 114 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 6478) covalent geometry : angle 0.55746 / 0.29 ( 8816) SS BOND : bond 0.00510 / 0.25 ( 4) SS BOND : angle 0.95713 / 0.57 ( 8) hydrogen bonds : bond 0.03974 / 2.63 ( 347) hydrogen bonds : angle 4.72170 / 3.48 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.237 Fit side-chains REVERT: A 244 GLU cc_start: 0.7963 (pp20) cc_final: 0.7449 (tm-30) REVERT: L 211 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7252 (mtm110) REVERT: H 89 ASP cc_start: 0.8715 (t0) cc_final: 0.8495 (t0) outliers start: 26 outliers final: 26 residues processed: 91 average time/residue: 0.0716 time to fit residues: 8.9172 Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 chunk 44 optimal weight: 0.0170 chunk 77 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100555 restraints weight = 8155.734| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.16 r_work: 0.3086 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6482 Z= 0.100 Angle : 0.512 6.375 8824 Z= 0.264 Chirality : 0.040 0.137 1018 Planarity : 0.004 0.043 1103 Dihedral : 4.154 20.998 884 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.85 % Allowed : 23.33 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 1.00 (0.30), residues: 822 helix: 1.60 (0.30), residues: 337 sheet: 1.12 (0.35), residues: 215 loop : -0.91 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.009 0.001 TYR L 49 PHE 0.009 0.001 PHE L 87 TRP 0.011 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 6478) covalent geometry : angle 0.51154 / 0.26 ( 8816) SS BOND : bond 0.00420 / 0.21 ( 4) SS BOND : angle 0.67134 / 0.40 ( 8) hydrogen bonds : bond 0.02981 / 1.97 ( 347) hydrogen bonds : angle 4.45773 / 3.29 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.66 seconds wall clock time: 26 minutes 37.82 seconds (1597.82 seconds total)