Starting phenix.real_space_refine on Thu Jun 5 09:58:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgm_41241/06_2025/8tgm_41241_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgm_41241/06_2025/8tgm_41241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tgm_41241/06_2025/8tgm_41241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgm_41241/06_2025/8tgm_41241.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgm_41241/06_2025/8tgm_41241_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgm_41241/06_2025/8tgm_41241_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 58 5.16 5 C 3878 2.51 5 N 900 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5826 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2869 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2869 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.86 Number of scatterers: 5826 At special positions: 0 Unit cell: (73.04, 65.736, 114.872, 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 58 16.00 O 990 8.00 N 900 7.00 C 3878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.35 Conformation dependent library (CDL) restraints added in 799.6 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.738A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.004A pdb=" N GLU A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 Proline residue: A 155 - end of helix removed outlier: 4.369A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 189 through 219 removed outlier: 3.683A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 4.082A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix removed outlier: 4.051A pdb=" N SER A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.533A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 299 through 318 removed outlier: 3.895A pdb=" N ALA A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.877A pdb=" N LEU A 338 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY A 339 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 3.664A pdb=" N TYR A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.542A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 422 removed outlier: 4.155A pdb=" N MET A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 455 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 456 through 472 removed outlier: 3.692A pdb=" N LEU A 460 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.535A pdb=" N ARG A 479 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 54 removed outlier: 3.971A pdb=" N VAL B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Proline residue: B 46 - end of helix removed outlier: 3.720A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 165 removed outlier: 4.098A pdb=" N GLU B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.338A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.523A pdb=" N MET B 170 " --> pdb=" O TYR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.861A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 244 removed outlier: 3.765A pdb=" N GLY B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 254 removed outlier: 3.782A pdb=" N GLU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.593A pdb=" N LEU B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 318 removed outlier: 3.511A pdb=" N ALA B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.505A pdb=" N ALA B 341 " --> pdb=" O LEU B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 342 through 360 removed outlier: 3.835A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.522A pdb=" N CYS B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 422 removed outlier: 4.115A pdb=" N MET B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.681A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.875A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 3.700A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.634A pdb=" N TYR B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 479 " --> pdb=" O TYR B 476 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1296 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: 1.55 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 868 1.29 - 1.42: 1554 1.42 - 1.55: 3447 1.55 - 1.68: 3 1.68 - 1.81: 102 Bond restraints: 5974 Sorted by residual: bond pdb=" C PRO A 481 " pdb=" O PRO A 481 " ideal model delta sigma weight residual 1.240 1.161 0.080 1.12e-02 7.97e+03 5.06e+01 bond pdb=" C31 YHR A 601 " pdb=" O30 YHR A 601 " ideal model delta sigma weight residual 1.326 1.406 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.403 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C17 YHR B 601 " pdb=" O19 YHR B 601 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C PRO B 481 " pdb=" O PRO B 481 " ideal model delta sigma weight residual 1.240 1.200 0.041 1.12e-02 7.97e+03 1.33e+01 ... (remaining 5969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 8048 3.77 - 7.54: 80 7.54 - 11.31: 10 11.31 - 15.07: 0 15.07 - 18.84: 2 Bond angle restraints: 8140 Sorted by residual: angle pdb=" C PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta sigma weight residual 111.46 102.41 9.05 1.29e+00 6.01e-01 4.92e+01 angle pdb=" N ARG B 225 " pdb=" CA ARG B 225 " pdb=" C ARG B 225 " ideal model delta sigma weight residual 111.28 104.37 6.91 1.09e+00 8.42e-01 4.02e+01 angle pdb=" C7 YHR A 601 " pdb=" N8 YHR A 601 " pdb=" C9 YHR A 601 " ideal model delta sigma weight residual 111.89 130.73 -18.84 3.00e+00 1.11e-01 3.95e+01 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 130.67 -18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb=" C PRO A 481 " pdb=" N PRO A 482 " pdb=" CA PRO A 482 " ideal model delta sigma weight residual 120.98 115.56 5.42 1.07e+00 8.73e-01 2.56e+01 ... (remaining 8135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.89: 3150 22.89 - 45.78: 333 45.78 - 68.66: 35 68.66 - 91.55: 14 91.55 - 114.44: 2 Dihedral angle restraints: 3534 sinusoidal: 1380 harmonic: 2154 Sorted by residual: dihedral pdb=" C PRO B 482 " pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta harmonic sigma weight residual -120.70 -110.63 -10.07 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" C13 YHR A 601 " pdb=" C7 YHR A 601 " pdb=" N8 YHR A 601 " pdb=" C6 YHR A 601 " ideal model delta sinusoidal sigma weight residual 57.66 -56.78 114.44 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 57.66 -56.10 113.76 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 3531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 874 0.082 - 0.165: 93 0.165 - 0.247: 4 0.247 - 0.329: 1 0.329 - 0.411: 2 Chirality restraints: 974 Sorted by residual: chirality pdb=" C13 YHR A 601 " pdb=" C12 YHR A 601 " pdb=" C14 YHR A 601 " pdb=" N8 YHR A 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.70 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.69 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA PHE A 131 " pdb=" N PHE A 131 " pdb=" C PHE A 131 " pdb=" CB PHE A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 971 not shown) Planarity restraints: 988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 472 " 0.062 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO B 473 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 426 " 0.015 2.00e-02 2.50e+03 2.16e-02 9.33e+00 pdb=" CG TYR A 426 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 426 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 426 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 426 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 426 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 426 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 426 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 42 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO B 43 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " 0.041 5.00e-02 4.00e+02 ... (remaining 985 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1653 2.80 - 3.33: 5569 3.33 - 3.85: 9526 3.85 - 4.38: 10285 4.38 - 4.90: 18577 Nonbonded interactions: 45610 Sorted by model distance: nonbonded pdb=" O THR B 291 " pdb=" OG1 THR B 291 " model vdw 2.279 3.040 nonbonded pdb=" OE1 GLU A 135 " pdb=" NH1 ARG A 138 " model vdw 2.283 3.120 nonbonded pdb=" O ARG A 365 " pdb=" OG SER A 409 " model vdw 2.309 3.040 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 161 " model vdw 2.325 3.040 nonbonded pdb=" OG1 THR A 291 " pdb=" O THR A 423 " model vdw 2.347 3.040 ... (remaining 45605 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.120 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 0.080 5974 Z= 0.348 Angle : 0.973 18.843 8140 Z= 0.523 Chirality : 0.052 0.411 974 Planarity : 0.009 0.094 988 Dihedral : 17.986 114.441 2166 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.83 % Rotamer: Outliers : 0.65 % Allowed : 32.41 % Favored : 66.94 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 756 helix: 1.09 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.73 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.005 0.001 HIS A 387 PHE 0.019 0.002 PHE B 265 TYR 0.052 0.002 TYR A 426 ARG 0.010 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.14516 ( 442) hydrogen bonds : angle 5.39266 ( 1296) covalent geometry : bond 0.00655 ( 5974) covalent geometry : angle 0.97298 ( 8140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.595 Fit side-chains REVERT: A 439 MET cc_start: 0.8235 (tpp) cc_final: 0.7662 (mpp) REVERT: B 163 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7453 (mtp180) REVERT: B 229 MET cc_start: 0.7887 (mmm) cc_final: 0.7625 (mmm) REVERT: B 373 MET cc_start: 0.7738 (mtp) cc_final: 0.7413 (mtp) REVERT: B 482 PRO cc_start: 0.8860 (Cg_exo) cc_final: 0.8607 (Cg_endo) outliers start: 4 outliers final: 3 residues processed: 138 average time/residue: 0.1163 time to fit residues: 23.2200 Evaluate side-chains 130 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 163 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 329 GLN B 35 ASN B 329 GLN B 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099756 restraints weight = 8113.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102807 restraints weight = 3850.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104795 restraints weight = 2220.343| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5974 Z= 0.157 Angle : 0.686 7.552 8140 Z= 0.328 Chirality : 0.043 0.157 974 Planarity : 0.006 0.057 988 Dihedral : 7.076 54.674 944 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.07 % Allowed : 28.18 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.31), residues: 756 helix: 1.80 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.50 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 459 HIS 0.001 0.000 HIS A 416 PHE 0.014 0.001 PHE A 356 TYR 0.010 0.001 TYR B 476 ARG 0.004 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.05365 ( 442) hydrogen bonds : angle 4.21088 ( 1296) covalent geometry : bond 0.00355 ( 5974) covalent geometry : angle 0.68619 ( 8140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.562 Fit side-chains REVERT: A 168 ILE cc_start: 0.8170 (mp) cc_final: 0.7938 (mm) REVERT: A 174 PHE cc_start: 0.7968 (t80) cc_final: 0.7693 (t80) REVERT: A 381 LEU cc_start: 0.8169 (mp) cc_final: 0.7759 (mp) REVERT: B 229 MET cc_start: 0.7602 (mmm) cc_final: 0.7204 (mmm) REVERT: B 236 LEU cc_start: 0.7686 (mt) cc_final: 0.7470 (mt) REVERT: B 261 LEU cc_start: 0.7793 (mm) cc_final: 0.7537 (mm) REVERT: B 373 MET cc_start: 0.7289 (mtp) cc_final: 0.6911 (mtp) outliers start: 25 outliers final: 5 residues processed: 149 average time/residue: 0.1326 time to fit residues: 28.0655 Evaluate side-chains 137 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN B 313 ASN B 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099014 restraints weight = 8471.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102283 restraints weight = 3948.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104399 restraints weight = 2249.488| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5974 Z= 0.164 Angle : 0.666 7.009 8140 Z= 0.320 Chirality : 0.044 0.210 974 Planarity : 0.006 0.046 988 Dihedral : 6.273 51.597 938 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.91 % Allowed : 27.85 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.31), residues: 756 helix: 1.76 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.22 (0.42), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.018 0.001 PHE A 356 TYR 0.011 0.001 TYR B 476 ARG 0.003 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.05273 ( 442) hydrogen bonds : angle 4.15089 ( 1296) covalent geometry : bond 0.00377 ( 5974) covalent geometry : angle 0.66563 ( 8140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.627 Fit side-chains REVERT: A 168 ILE cc_start: 0.8118 (mp) cc_final: 0.7899 (mm) REVERT: A 174 PHE cc_start: 0.8027 (t80) cc_final: 0.7725 (t80) REVERT: A 296 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 381 LEU cc_start: 0.8171 (mp) cc_final: 0.7885 (mp) REVERT: B 261 LEU cc_start: 0.7780 (mm) cc_final: 0.7529 (mm) REVERT: B 274 GLN cc_start: 0.7602 (pt0) cc_final: 0.7118 (pt0) REVERT: B 295 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6355 (mpp) REVERT: B 373 MET cc_start: 0.7348 (mtp) cc_final: 0.7013 (mtp) outliers start: 24 outliers final: 8 residues processed: 146 average time/residue: 0.1255 time to fit residues: 26.1128 Evaluate side-chains 141 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104534 restraints weight = 8187.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107300 restraints weight = 4001.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109070 restraints weight = 2354.525| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5974 Z= 0.163 Angle : 0.658 7.993 8140 Z= 0.315 Chirality : 0.044 0.147 974 Planarity : 0.005 0.043 988 Dihedral : 5.903 52.796 938 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.37 % Allowed : 27.36 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.31), residues: 756 helix: 1.86 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.11 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.018 0.001 PHE B 356 TYR 0.012 0.001 TYR B 476 ARG 0.005 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 442) hydrogen bonds : angle 4.09207 ( 1296) covalent geometry : bond 0.00378 ( 5974) covalent geometry : angle 0.65809 ( 8140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.614 Fit side-chains REVERT: A 43 PRO cc_start: 0.8453 (Cg_endo) cc_final: 0.8232 (Cg_exo) REVERT: A 163 ARG cc_start: 0.6568 (mtp180) cc_final: 0.6200 (mpp-170) REVERT: A 174 PHE cc_start: 0.7898 (t80) cc_final: 0.7677 (t80) REVERT: A 340 LEU cc_start: 0.7759 (mt) cc_final: 0.7385 (mp) REVERT: A 381 LEU cc_start: 0.8377 (mp) cc_final: 0.8049 (mp) REVERT: B 261 LEU cc_start: 0.7774 (mm) cc_final: 0.7558 (mm) REVERT: B 295 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6445 (mpp) REVERT: B 373 MET cc_start: 0.7200 (mtp) cc_final: 0.6872 (mtp) outliers start: 33 outliers final: 15 residues processed: 155 average time/residue: 0.1279 time to fit residues: 28.4267 Evaluate side-chains 149 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 0.0060 chunk 15 optimal weight: 0.4980 chunk 57 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104659 restraints weight = 8006.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107605 restraints weight = 3873.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109464 restraints weight = 2264.188| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5974 Z= 0.135 Angle : 0.633 6.680 8140 Z= 0.303 Chirality : 0.043 0.170 974 Planarity : 0.005 0.043 988 Dihedral : 5.653 53.776 938 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.03 % Allowed : 27.04 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.31), residues: 756 helix: 1.91 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.17 (0.42), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.018 0.001 PHE B 356 TYR 0.009 0.001 TYR B 190 ARG 0.002 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 442) hydrogen bonds : angle 4.04956 ( 1296) covalent geometry : bond 0.00297 ( 5974) covalent geometry : angle 0.63281 ( 8140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.602 Fit side-chains REVERT: A 40 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7590 (p) REVERT: A 43 PRO cc_start: 0.8533 (Cg_endo) cc_final: 0.8326 (Cg_exo) REVERT: A 163 ARG cc_start: 0.6600 (mtp180) cc_final: 0.6271 (mpp-170) REVERT: A 174 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7645 (t80) REVERT: A 245 PRO cc_start: 0.8478 (Cg_endo) cc_final: 0.8233 (Cg_exo) REVERT: A 340 LEU cc_start: 0.7727 (mt) cc_final: 0.7393 (mp) REVERT: A 381 LEU cc_start: 0.8355 (mp) cc_final: 0.8024 (mp) REVERT: B 245 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7886 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7707 (mm) cc_final: 0.7502 (mm) REVERT: B 295 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6462 (mpp) REVERT: B 373 MET cc_start: 0.7248 (mtp) cc_final: 0.6896 (mtp) outliers start: 37 outliers final: 14 residues processed: 152 average time/residue: 0.1149 time to fit residues: 25.3781 Evaluate side-chains 150 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 67 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097567 restraints weight = 8222.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100521 restraints weight = 3955.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102478 restraints weight = 2308.052| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5974 Z= 0.142 Angle : 0.625 6.708 8140 Z= 0.300 Chirality : 0.043 0.149 974 Planarity : 0.005 0.037 988 Dihedral : 5.549 54.893 936 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.40 % Allowed : 28.50 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.31), residues: 756 helix: 1.95 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.08 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.019 0.001 PHE B 356 TYR 0.010 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 442) hydrogen bonds : angle 3.99323 ( 1296) covalent geometry : bond 0.00322 ( 5974) covalent geometry : angle 0.62550 ( 8140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.538 Fit side-chains REVERT: A 43 PRO cc_start: 0.8544 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: A 163 ARG cc_start: 0.6610 (mtp180) cc_final: 0.6298 (mpp-170) REVERT: A 174 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7621 (t80) REVERT: A 245 PRO cc_start: 0.8458 (Cg_endo) cc_final: 0.8241 (Cg_exo) REVERT: A 340 LEU cc_start: 0.7724 (mt) cc_final: 0.7396 (mp) REVERT: A 381 LEU cc_start: 0.8358 (mp) cc_final: 0.8028 (mp) REVERT: A 479 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6746 (ptt-90) REVERT: B 229 MET cc_start: 0.7972 (mmm) cc_final: 0.7156 (mmm) REVERT: B 261 LEU cc_start: 0.7785 (mm) cc_final: 0.7571 (mm) REVERT: B 295 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6446 (mpp) REVERT: B 373 MET cc_start: 0.7282 (mtp) cc_final: 0.6888 (mtp) REVERT: B 423 THR cc_start: 0.8325 (m) cc_final: 0.8024 (p) outliers start: 27 outliers final: 14 residues processed: 151 average time/residue: 0.1246 time to fit residues: 26.8257 Evaluate side-chains 152 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 15 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.0020 chunk 47 optimal weight: 0.9980 overall best weight: 0.2906 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.113711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102374 restraints weight = 8248.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105346 restraints weight = 4001.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107292 restraints weight = 2334.442| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5974 Z= 0.126 Angle : 0.612 6.810 8140 Z= 0.295 Chirality : 0.042 0.148 974 Planarity : 0.005 0.051 988 Dihedral : 5.535 54.395 936 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.58 % Allowed : 30.46 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.31), residues: 756 helix: 2.05 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.03 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.015 0.001 PHE A 356 TYR 0.009 0.001 TYR B 190 ARG 0.002 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 442) hydrogen bonds : angle 3.98820 ( 1296) covalent geometry : bond 0.00274 ( 5974) covalent geometry : angle 0.61242 ( 8140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.591 Fit side-chains REVERT: A 174 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 340 LEU cc_start: 0.7655 (mt) cc_final: 0.7355 (mp) REVERT: A 381 LEU cc_start: 0.8339 (mp) cc_final: 0.8012 (mp) REVERT: A 479 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6704 (ptt-90) REVERT: B 229 MET cc_start: 0.7950 (mmm) cc_final: 0.7052 (mmm) REVERT: B 245 PRO cc_start: 0.8076 (Cg_endo) cc_final: 0.7851 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7703 (mm) cc_final: 0.7489 (mm) REVERT: B 295 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6486 (mpp) REVERT: B 373 MET cc_start: 0.7263 (mtp) cc_final: 0.6878 (mtp) REVERT: B 423 THR cc_start: 0.8312 (m) cc_final: 0.7996 (p) REVERT: B 428 SER cc_start: 0.7841 (p) cc_final: 0.7628 (m) outliers start: 22 outliers final: 13 residues processed: 150 average time/residue: 0.1231 time to fit residues: 26.4103 Evaluate side-chains 151 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 4 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.111761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100557 restraints weight = 8171.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103435 restraints weight = 4024.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105314 restraints weight = 2387.038| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5974 Z= 0.154 Angle : 0.634 7.018 8140 Z= 0.307 Chirality : 0.044 0.220 974 Planarity : 0.006 0.072 988 Dihedral : 5.584 55.656 936 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.91 % Allowed : 30.78 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.31), residues: 756 helix: 2.02 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.07 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.016 0.001 PHE B 246 TYR 0.012 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 442) hydrogen bonds : angle 4.02455 ( 1296) covalent geometry : bond 0.00361 ( 5974) covalent geometry : angle 0.63385 ( 8140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.607 Fit side-chains REVERT: A 174 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7665 (t80) REVERT: A 340 LEU cc_start: 0.7762 (mt) cc_final: 0.7420 (mp) REVERT: A 381 LEU cc_start: 0.8347 (mp) cc_final: 0.8030 (mp) REVERT: A 479 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6767 (ptt-90) REVERT: B 229 MET cc_start: 0.7999 (mmm) cc_final: 0.7239 (mmm) REVERT: B 245 PRO cc_start: 0.8104 (Cg_endo) cc_final: 0.7869 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7817 (mm) cc_final: 0.7588 (mm) REVERT: B 295 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6488 (mpp) REVERT: B 373 MET cc_start: 0.7286 (mtp) cc_final: 0.6934 (mtp) REVERT: B 423 THR cc_start: 0.8338 (m) cc_final: 0.8021 (p) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.1269 time to fit residues: 26.6719 Evaluate side-chains 152 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 0.1980 chunk 7 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 13 optimal weight: 0.0020 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.120136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109143 restraints weight = 7911.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112165 restraints weight = 3805.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114072 restraints weight = 2211.237| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5974 Z= 0.128 Angle : 0.621 7.562 8140 Z= 0.299 Chirality : 0.042 0.183 974 Planarity : 0.006 0.069 988 Dihedral : 5.620 55.983 936 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.42 % Allowed : 31.76 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.31), residues: 756 helix: 2.06 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.99 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS B 422 PHE 0.015 0.001 PHE A 356 TYR 0.009 0.001 TYR B 190 ARG 0.002 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 442) hydrogen bonds : angle 4.00693 ( 1296) covalent geometry : bond 0.00280 ( 5974) covalent geometry : angle 0.62107 ( 8140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.598 Fit side-chains REVERT: A 174 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7572 (t80) REVERT: A 340 LEU cc_start: 0.7701 (mt) cc_final: 0.7356 (mp) REVERT: A 381 LEU cc_start: 0.8349 (mp) cc_final: 0.8015 (mp) REVERT: A 479 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6749 (ptt-90) REVERT: B 229 MET cc_start: 0.7924 (mmm) cc_final: 0.7157 (mmm) REVERT: B 245 PRO cc_start: 0.8051 (Cg_endo) cc_final: 0.7808 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7726 (mm) cc_final: 0.7509 (mm) REVERT: B 295 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6481 (mpp) REVERT: B 370 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7539 (tt) REVERT: B 373 MET cc_start: 0.7272 (mtp) cc_final: 0.6912 (mtp) REVERT: B 423 THR cc_start: 0.8294 (m) cc_final: 0.8048 (p) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.1300 time to fit residues: 25.0919 Evaluate side-chains 147 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.116708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105842 restraints weight = 8102.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108796 restraints weight = 3901.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110696 restraints weight = 2281.103| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5974 Z= 0.166 Angle : 0.647 8.149 8140 Z= 0.312 Chirality : 0.044 0.165 974 Planarity : 0.006 0.064 988 Dihedral : 5.701 57.704 936 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.42 % Allowed : 31.92 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.31), residues: 756 helix: 1.98 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.03 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.019 0.001 PHE B 246 TYR 0.013 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.05018 ( 442) hydrogen bonds : angle 4.04341 ( 1296) covalent geometry : bond 0.00390 ( 5974) covalent geometry : angle 0.64736 ( 8140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.609 Fit side-chains REVERT: A 174 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7699 (t80) REVERT: A 340 LEU cc_start: 0.7777 (mt) cc_final: 0.7420 (mp) REVERT: A 381 LEU cc_start: 0.8377 (mp) cc_final: 0.8061 (mp) REVERT: A 479 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6836 (ptt-90) REVERT: B 141 VAL cc_start: 0.7727 (p) cc_final: 0.7510 (t) REVERT: B 229 MET cc_start: 0.7948 (mmm) cc_final: 0.7203 (mmm) REVERT: B 245 PRO cc_start: 0.8130 (Cg_endo) cc_final: 0.7859 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7862 (mm) cc_final: 0.7621 (mm) REVERT: B 295 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6490 (mpp) REVERT: B 373 MET cc_start: 0.7250 (mtp) cc_final: 0.6915 (mtp) REVERT: B 423 THR cc_start: 0.8324 (m) cc_final: 0.8066 (p) outliers start: 21 outliers final: 15 residues processed: 138 average time/residue: 0.1289 time to fit residues: 25.1839 Evaluate side-chains 148 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.117189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106374 restraints weight = 7999.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109329 restraints weight = 3871.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111252 restraints weight = 2264.445| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5974 Z= 0.154 Angle : 0.644 8.077 8140 Z= 0.310 Chirality : 0.044 0.156 974 Planarity : 0.006 0.063 988 Dihedral : 5.708 58.768 936 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.26 % Allowed : 32.25 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.31), residues: 756 helix: 1.98 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.03 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS A 422 PHE 0.018 0.001 PHE B 246 TYR 0.012 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 442) hydrogen bonds : angle 4.06079 ( 1296) covalent geometry : bond 0.00357 ( 5974) covalent geometry : angle 0.64446 ( 8140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.71 seconds wall clock time: 42 minutes 2.40 seconds (2522.40 seconds total)