Starting phenix.real_space_refine on Sat Aug 23 03:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8if8_35410/08_2025/8if8_35410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8if8_35410/08_2025/8if8_35410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8if8_35410/08_2025/8if8_35410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8if8_35410/08_2025/8if8_35410.map" model { file = "/net/cci-nas-00/data/ceres_data/8if8_35410/08_2025/8if8_35410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8if8_35410/08_2025/8if8_35410.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 34 5.16 5 C 6093 2.51 5 N 1593 2.21 5 O 1585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9307 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4569 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 34, 'TRANS': 563} Chain breaks: 2 Chain: "B" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4736 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 37, 'TRANS': 582} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.50, per 1000 atoms: 0.27 Number of scatterers: 9307 At special positions: 0 Unit cell: (101.504, 86.528, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 34 16.00 O 1585 8.00 N 1593 7.00 C 6093 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: 0.74 Conformation dependent library (CDL) restraints added in 327.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 3 sheets defined 67.0% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 21 through 53 removed outlier: 4.147A pdb=" N VAL C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 88 removed outlier: 3.536A pdb=" N LEU C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS C 88 " --> pdb=" O TRP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 113 removed outlier: 3.543A pdb=" N MET C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 removed outlier: 3.754A pdb=" N ARG C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 141 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 142 " --> pdb=" O ARG C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 172 removed outlier: 3.517A pdb=" N ILE C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 203 Processing helix chain 'C' and resid 204 through 224 removed outlier: 3.958A pdb=" N SER C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 235 through 249 removed outlier: 3.591A pdb=" N MET C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 270 removed outlier: 3.886A pdb=" N VAL C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 270 " --> pdb=" O GLY C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 294 removed outlier: 3.542A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 298 removed outlier: 3.748A pdb=" N GLY C 298 " --> pdb=" O LEU C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 298' Processing helix chain 'C' and resid 303 through 331 removed outlier: 4.339A pdb=" N THR C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Proline residue: C 326 - end of helix removed outlier: 3.504A pdb=" N ARG C 330 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 378 Processing helix chain 'C' and resid 381 through 405 removed outlier: 3.531A pdb=" N MET C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 416 through 442 removed outlier: 4.030A pdb=" N ARG C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 463 removed outlier: 4.095A pdb=" N MET C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 497 through 510 Processing helix chain 'C' and resid 512 through 515 removed outlier: 3.625A pdb=" N ARG C 515 " --> pdb=" O ARG C 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 512 through 515' Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 547 through 559 Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.605A pdb=" N ASP C 572 " --> pdb=" O ILE C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 621 removed outlier: 4.288A pdb=" N ASP C 621 " --> pdb=" O LEU C 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 51 removed outlier: 3.636A pdb=" N LEU B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 62 through 88 removed outlier: 3.665A pdb=" N THR B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 79 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS B 88 " --> pdb=" O TRP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 113 removed outlier: 3.620A pdb=" N MET B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.988A pdb=" N ARG B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 172 removed outlier: 3.534A pdb=" N ILE B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.579A pdb=" N VAL B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 222 removed outlier: 3.555A pdb=" N ALA B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 248 removed outlier: 4.169A pdb=" N ILE B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Proline residue: B 237 - end of helix removed outlier: 4.011A pdb=" N GLY B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 248 " --> pdb=" O TRP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.622A pdb=" N VAL B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 294 Processing helix chain 'B' and resid 303 through 320 removed outlier: 3.624A pdb=" N ALA B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.588A pdb=" N ALA B 351 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 352 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 378 Processing helix chain 'B' and resid 381 through 405 removed outlier: 3.538A pdb=" N ALA B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 412 through 415 Processing helix chain 'B' and resid 416 through 440 Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 493 through 496 removed outlier: 3.979A pdb=" N LYS B 496 " --> pdb=" O GLY B 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 493 through 496' Processing helix chain 'B' and resid 497 through 510 Processing helix chain 'B' and resid 524 through 529 removed outlier: 3.770A pdb=" N TYR B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 547 through 558 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 563 through 571 Processing sheet with id=AA1, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.683A pdb=" N MET C 584 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 532 through 533 removed outlier: 19.774A pdb=" N VAL B 581 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 16.100A pdb=" N ALA B 597 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N LEU B 583 " --> pdb=" O ARG B 595 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ARG B 595 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 532 through 533 588 hydrogen bonds defined for protein. 1719 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: 1.31 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1408 1.32 - 1.44: 2694 1.44 - 1.56: 5389 1.56 - 1.68: 0 1.68 - 1.81: 62 Bond restraints: 9553 Sorted by residual: bond pdb=" CA SER C 224 " pdb=" CB SER C 224 " ideal model delta sigma weight residual 1.530 1.447 0.083 1.58e-02 4.01e+03 2.77e+01 bond pdb=" N GLN B 604 " pdb=" CA GLN B 604 " ideal model delta sigma weight residual 1.462 1.496 -0.034 7.70e-03 1.69e+04 1.95e+01 bond pdb=" CA SER B 361 " pdb=" CB SER B 361 " ideal model delta sigma weight residual 1.530 1.464 0.066 1.93e-02 2.68e+03 1.16e+01 bond pdb=" C TYR B 592 " pdb=" O TYR B 592 " ideal model delta sigma weight residual 1.234 1.196 0.038 1.16e-02 7.43e+03 1.09e+01 bond pdb=" N TYR B 601 " pdb=" CA TYR B 601 " ideal model delta sigma weight residual 1.462 1.487 -0.025 7.70e-03 1.69e+04 1.06e+01 ... (remaining 9548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 12950 3.43 - 6.87: 106 6.87 - 10.30: 16 10.30 - 13.73: 0 13.73 - 17.17: 1 Bond angle restraints: 13073 Sorted by residual: angle pdb=" N PRO B 605 " pdb=" CA PRO B 605 " pdb=" C PRO B 605 " ideal model delta sigma weight residual 112.47 95.30 17.17 2.06e+00 2.36e-01 6.95e+01 angle pdb=" CA TYR B 601 " pdb=" C TYR B 601 " pdb=" O TYR B 601 " ideal model delta sigma weight residual 119.08 111.61 7.47 9.50e-01 1.11e+00 6.19e+01 angle pdb=" N ARG C 201 " pdb=" CA ARG C 201 " pdb=" C ARG C 201 " ideal model delta sigma weight residual 113.41 105.23 8.18 1.22e+00 6.72e-01 4.49e+01 angle pdb=" CA TYR B 601 " pdb=" C TYR B 601 " pdb=" N PRO B 602 " ideal model delta sigma weight residual 120.52 125.69 -5.17 8.30e-01 1.45e+00 3.87e+01 angle pdb=" N ASN B 606 " pdb=" CA ASN B 606 " pdb=" CB ASN B 606 " ideal model delta sigma weight residual 110.32 100.64 9.68 1.70e+00 3.46e-01 3.24e+01 ... (remaining 13068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5075 17.72 - 35.45: 388 35.45 - 53.17: 72 53.17 - 70.89: 10 70.89 - 88.61: 4 Dihedral angle restraints: 5549 sinusoidal: 2057 harmonic: 3492 Sorted by residual: dihedral pdb=" N ASN B 606 " pdb=" C ASN B 606 " pdb=" CA ASN B 606 " pdb=" CB ASN B 606 " ideal model delta harmonic sigma weight residual 122.80 109.79 13.01 0 2.50e+00 1.60e-01 2.71e+01 dihedral pdb=" CA ALA B 317 " pdb=" C ALA B 317 " pdb=" N ALA B 318 " pdb=" CA ALA B 318 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" N TRP C 200 " pdb=" C TRP C 200 " pdb=" CA TRP C 200 " pdb=" CB TRP C 200 " ideal model delta harmonic sigma weight residual 122.80 134.65 -11.85 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 5546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1380 0.080 - 0.161: 134 0.161 - 0.241: 6 0.241 - 0.321: 2 0.321 - 0.402: 5 Chirality restraints: 1527 Sorted by residual: chirality pdb=" CA ASN B 606 " pdb=" N ASN B 606 " pdb=" C ASN B 606 " pdb=" CB ASN B 606 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA TRP C 200 " pdb=" N TRP C 200 " pdb=" C TRP C 200 " pdb=" CB TRP C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA VAL B 600 " pdb=" N VAL B 600 " pdb=" C VAL B 600 " pdb=" CB VAL B 600 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 1524 not shown) Planarity restraints: 1627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 200 " -0.035 2.00e-02 2.50e+03 2.99e-02 2.23e+01 pdb=" CG TRP B 200 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP B 200 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 200 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 200 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 200 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 155 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO B 155 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO B 155 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE B 156 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 357 " -0.016 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C MET B 357 " 0.059 2.00e-02 2.50e+03 pdb=" O MET B 357 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 358 " -0.020 2.00e-02 2.50e+03 ... (remaining 1624 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1822 2.77 - 3.30: 8734 3.30 - 3.83: 15141 3.83 - 4.37: 17613 4.37 - 4.90: 31877 Nonbonded interactions: 75187 Sorted by model distance: nonbonded pdb=" O MET C 402 " pdb=" OG1 THR C 405 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR C 157 " pdb=" OH TYR C 228 " model vdw 2.243 3.040 nonbonded pdb=" O ASP B 514 " pdb=" NE1 TRP B 532 " model vdw 2.285 3.120 nonbonded pdb=" O LEU B 136 " pdb=" OG1 THR B 140 " model vdw 2.318 3.040 nonbonded pdb=" NE1 TRP C 373 " pdb=" OE1 GLU C 434 " model vdw 2.326 3.120 ... (remaining 75182 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 21 through 339 or resid 351 through 598 or resid 609 throu \ gh 701)) selection = chain 'C' } 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: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.480 Find NCS groups from input model: 0.220 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 0.083 9553 Z= 0.302 Angle : 0.813 17.168 13073 Z= 0.474 Chirality : 0.052 0.402 1527 Planarity : 0.005 0.048 1627 Dihedral : 13.080 88.613 3317 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.25), residues: 1210 helix: 1.24 (0.20), residues: 746 sheet: -0.87 (0.74), residues: 54 loop : -2.30 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 442 TYR 0.044 0.002 TYR B 135 PHE 0.025 0.002 PHE C 414 TRP 0.081 0.002 TRP B 200 HIS 0.004 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 9553) covalent geometry : angle 0.81286 (13073) hydrogen bonds : bond 0.13813 ( 584) hydrogen bonds : angle 5.61806 ( 1719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.369 Fit side-chains REVERT: C 415 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7413 (mtp180) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1168 time to fit residues: 15.2982 Evaluate side-chains 79 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099443 restraints weight = 12470.024| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.12 r_work: 0.3178 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9553 Z= 0.131 Angle : 0.585 8.641 13073 Z= 0.295 Chirality : 0.041 0.179 1527 Planarity : 0.005 0.046 1627 Dihedral : 4.411 24.346 1345 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.43 % Allowed : 7.07 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1210 helix: 1.77 (0.20), residues: 751 sheet: -0.74 (0.74), residues: 54 loop : -2.06 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 442 TYR 0.018 0.001 TYR C 135 PHE 0.013 0.001 PHE C 267 TRP 0.041 0.001 TRP B 200 HIS 0.003 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9553) covalent geometry : angle 0.58507 (13073) hydrogen bonds : bond 0.04558 ( 584) hydrogen bonds : angle 3.75397 ( 1719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.356 Fit side-chains REVERT: C 415 ARG cc_start: 0.7928 (mtp85) cc_final: 0.7470 (mtp180) REVERT: B 573 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8745 (ttmm) outliers start: 4 outliers final: 2 residues processed: 92 average time/residue: 0.0949 time to fit residues: 12.4875 Evaluate side-chains 84 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 538 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 GLN ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098812 restraints weight = 12578.388| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.14 r_work: 0.3171 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9553 Z= 0.145 Angle : 0.581 8.442 13073 Z= 0.289 Chirality : 0.041 0.185 1527 Planarity : 0.005 0.043 1627 Dihedral : 4.262 24.216 1345 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.18 % Allowed : 10.50 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.25), residues: 1210 helix: 1.88 (0.20), residues: 755 sheet: -0.60 (0.72), residues: 54 loop : -1.95 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.019 0.001 TYR B 135 PHE 0.013 0.001 PHE C 131 TRP 0.034 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9553) covalent geometry : angle 0.58093 (13073) hydrogen bonds : bond 0.04523 ( 584) hydrogen bonds : angle 3.58669 ( 1719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.367 Fit side-chains REVERT: C 228 TYR cc_start: 0.9331 (p90) cc_final: 0.9088 (p90) REVERT: B 573 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8737 (ttmm) outliers start: 11 outliers final: 4 residues processed: 94 average time/residue: 0.0855 time to fit residues: 11.7045 Evaluate side-chains 87 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097860 restraints weight = 12613.359| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.15 r_work: 0.3151 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9553 Z= 0.165 Angle : 0.584 8.617 13073 Z= 0.292 Chirality : 0.041 0.186 1527 Planarity : 0.005 0.047 1627 Dihedral : 4.261 24.163 1345 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.29 % Allowed : 11.68 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1210 helix: 1.91 (0.20), residues: 755 sheet: -0.53 (0.72), residues: 54 loop : -1.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 138 TYR 0.024 0.001 TYR B 135 PHE 0.014 0.001 PHE C 131 TRP 0.029 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9553) covalent geometry : angle 0.58423 (13073) hydrogen bonds : bond 0.04611 ( 584) hydrogen bonds : angle 3.54118 ( 1719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.292 Fit side-chains REVERT: C 441 LYS cc_start: 0.8583 (mmmt) cc_final: 0.7915 (mtmt) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.0903 time to fit residues: 12.2220 Evaluate side-chains 88 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098331 restraints weight = 12549.883| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.17 r_work: 0.3166 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9553 Z= 0.133 Angle : 0.566 8.218 13073 Z= 0.281 Chirality : 0.040 0.190 1527 Planarity : 0.004 0.045 1627 Dihedral : 4.150 24.222 1345 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.07 % Allowed : 12.43 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1210 helix: 2.04 (0.20), residues: 755 sheet: -0.50 (0.73), residues: 54 loop : -1.84 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.018 0.001 TYR B 135 PHE 0.012 0.001 PHE B 267 TRP 0.029 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9553) covalent geometry : angle 0.56578 (13073) hydrogen bonds : bond 0.04266 ( 584) hydrogen bonds : angle 3.43755 ( 1719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.335 Fit side-chains REVERT: C 23 ARG cc_start: 0.7484 (mmm-85) cc_final: 0.6741 (mpp-170) REVERT: C 441 LYS cc_start: 0.8520 (mmmt) cc_final: 0.7947 (mtmt) REVERT: B 459 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8079 (mp) REVERT: B 573 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8733 (ttmm) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.0950 time to fit residues: 12.8109 Evaluate side-chains 91 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 62 optimal weight: 0.0170 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 20 optimal weight: 0.0670 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.126778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101262 restraints weight = 12449.263| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.16 r_work: 0.3208 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9553 Z= 0.108 Angle : 0.535 7.709 13073 Z= 0.266 Chirality : 0.039 0.189 1527 Planarity : 0.004 0.047 1627 Dihedral : 3.942 23.764 1345 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.86 % Allowed : 13.08 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.26), residues: 1210 helix: 2.28 (0.20), residues: 753 sheet: -0.33 (0.74), residues: 54 loop : -1.75 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 415 TYR 0.010 0.001 TYR B 135 PHE 0.011 0.001 PHE B 267 TRP 0.028 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9553) covalent geometry : angle 0.53493 (13073) hydrogen bonds : bond 0.03682 ( 584) hydrogen bonds : angle 3.27355 ( 1719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.355 Fit side-chains REVERT: C 23 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6603 (mpp-170) REVERT: C 441 LYS cc_start: 0.8435 (mmmt) cc_final: 0.7989 (ttmt) REVERT: B 467 ASP cc_start: 0.8484 (m-30) cc_final: 0.8147 (m-30) REVERT: B 573 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8739 (ttmm) outliers start: 8 outliers final: 7 residues processed: 107 average time/residue: 0.0882 time to fit residues: 13.7732 Evaluate side-chains 97 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097413 restraints weight = 12623.013| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.18 r_work: 0.3149 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9553 Z= 0.165 Angle : 0.594 8.315 13073 Z= 0.292 Chirality : 0.042 0.190 1527 Planarity : 0.005 0.049 1627 Dihedral : 4.076 24.164 1345 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.50 % Allowed : 13.50 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1210 helix: 2.12 (0.19), residues: 755 sheet: -0.26 (0.75), residues: 54 loop : -1.76 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 138 TYR 0.023 0.001 TYR B 135 PHE 0.014 0.001 PHE C 131 TRP 0.032 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9553) covalent geometry : angle 0.59374 (13073) hydrogen bonds : bond 0.04530 ( 584) hydrogen bonds : angle 3.44554 ( 1719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.276 Fit side-chains REVERT: C 23 ARG cc_start: 0.7418 (mmm-85) cc_final: 0.6659 (mpp-170) REVERT: C 441 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8013 (ttmt) REVERT: B 573 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8731 (ttmm) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.0970 time to fit residues: 13.3523 Evaluate side-chains 97 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.0170 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100262 restraints weight = 12444.096| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.17 r_work: 0.3197 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9553 Z= 0.110 Angle : 0.546 7.882 13073 Z= 0.270 Chirality : 0.040 0.172 1527 Planarity : 0.004 0.052 1627 Dihedral : 3.934 23.781 1345 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.96 % Allowed : 14.04 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.26), residues: 1210 helix: 2.35 (0.19), residues: 753 sheet: -0.37 (0.73), residues: 54 loop : -1.70 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 415 TYR 0.011 0.001 TYR B 135 PHE 0.012 0.001 PHE B 267 TRP 0.035 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9553) covalent geometry : angle 0.54577 (13073) hydrogen bonds : bond 0.03833 ( 584) hydrogen bonds : angle 3.29263 ( 1719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.277 Fit side-chains REVERT: C 23 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.6598 (mpp-170) REVERT: C 441 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8050 (ttmt) REVERT: B 467 ASP cc_start: 0.8399 (m-30) cc_final: 0.8152 (m-30) REVERT: B 573 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8729 (ttmm) outliers start: 9 outliers final: 9 residues processed: 99 average time/residue: 0.0920 time to fit residues: 12.8950 Evaluate side-chains 100 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 0.7980 chunk 45 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105562 restraints weight = 12207.455| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.07 r_work: 0.3266 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9553 Z= 0.112 Angle : 0.548 7.927 13073 Z= 0.269 Chirality : 0.040 0.169 1527 Planarity : 0.004 0.053 1627 Dihedral : 3.827 23.801 1345 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.96 % Allowed : 14.36 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.26), residues: 1210 helix: 2.46 (0.19), residues: 753 sheet: -0.59 (0.71), residues: 56 loop : -1.62 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 415 TYR 0.011 0.001 TYR B 135 PHE 0.011 0.001 PHE B 267 TRP 0.033 0.001 TRP C 200 HIS 0.004 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9553) covalent geometry : angle 0.54837 (13073) hydrogen bonds : bond 0.03720 ( 584) hydrogen bonds : angle 3.23685 ( 1719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.364 Fit side-chains REVERT: C 23 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6561 (mpp-170) REVERT: C 412 LEU cc_start: 0.8682 (mt) cc_final: 0.8307 (tp) REVERT: C 441 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8047 (ttmt) REVERT: B 467 ASP cc_start: 0.8354 (m-30) cc_final: 0.8115 (m-30) REVERT: B 573 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8736 (ttmm) outliers start: 9 outliers final: 8 residues processed: 102 average time/residue: 0.1098 time to fit residues: 15.4761 Evaluate side-chains 102 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 0.0020 chunk 108 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104233 restraints weight = 12375.983| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.05 r_work: 0.3258 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9553 Z= 0.123 Angle : 0.553 8.495 13073 Z= 0.271 Chirality : 0.040 0.177 1527 Planarity : 0.004 0.055 1627 Dihedral : 3.862 23.832 1345 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.96 % Allowed : 14.47 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.26), residues: 1210 helix: 2.45 (0.19), residues: 753 sheet: -0.58 (0.71), residues: 56 loop : -1.62 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 415 TYR 0.014 0.001 TYR B 222 PHE 0.012 0.001 PHE C 267 TRP 0.030 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9553) covalent geometry : angle 0.55307 (13073) hydrogen bonds : bond 0.03894 ( 584) hydrogen bonds : angle 3.26741 ( 1719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.351 Fit side-chains REVERT: C 23 ARG cc_start: 0.7313 (mmm-85) cc_final: 0.6575 (mpp-170) REVERT: C 412 LEU cc_start: 0.8687 (mt) cc_final: 0.8324 (tp) REVERT: C 441 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8063 (ttmt) REVERT: B 467 ASP cc_start: 0.8364 (m-30) cc_final: 0.8128 (m-30) REVERT: B 573 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8731 (ttmm) outliers start: 9 outliers final: 9 residues processed: 96 average time/residue: 0.1015 time to fit residues: 13.7324 Evaluate side-chains 99 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102575 restraints weight = 12284.021| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.04 r_work: 0.3238 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9553 Z= 0.142 Angle : 0.574 8.618 13073 Z= 0.281 Chirality : 0.041 0.187 1527 Planarity : 0.004 0.055 1627 Dihedral : 3.923 23.974 1345 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.29 % Allowed : 14.36 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.26), residues: 1210 helix: 2.38 (0.19), residues: 756 sheet: -0.62 (0.71), residues: 56 loop : -1.61 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 415 TYR 0.017 0.001 TYR B 135 PHE 0.012 0.001 PHE C 267 TRP 0.028 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9553) covalent geometry : angle 0.57373 (13073) hydrogen bonds : bond 0.04177 ( 584) hydrogen bonds : angle 3.33450 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.04 seconds wall clock time: 37 minutes 57.38 seconds (2277.38 seconds total)