Starting phenix.real_space_refine on Thu Mar 13 23:21:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8if8_35410/03_2025/8if8_35410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8if8_35410/03_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_35410/03_2025/8if8_35410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8if8_35410/03_2025/8if8_35410.map" model { file = "/net/cci-nas-00/data/ceres_data/8if8_35410/03_2025/8if8_35410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8if8_35410/03_2025/8if8_35410.cif" } resolution = 3.1 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= 0.061 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.29, per 1000 atoms: 0.78 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: 3.26 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.02 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: 3.05 Time building geometry restraints manager: 3.79 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 639 or resid 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: 4.160 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.630 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:4.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.170 ------------------------------------------------------------------------------- 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= 0.439 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 (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: -0.00 (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 TRP 0.081 0.002 TRP B 200 HIS 0.004 0.001 HIS C 540 PHE 0.025 0.002 PHE C 414 TYR 0.044 0.002 TYR B 135 ARG 0.004 0.000 ARG C 442 *********************** 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 : 0.999 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: 0.2573 time to fit residues: 33.7650 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 : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.123832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098680 restraints weight = 12422.005| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.12 r_work: 0.3167 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0787 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= 0.209 Angle : 0.594 8.769 13073 Z= 0.300 Chirality : 0.041 0.195 1527 Planarity : 0.005 0.047 1627 Dihedral : 4.445 24.407 1345 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.54 % Allowed : 7.07 % Favored : 92.39 % 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: 0.61 (0.26), residues: 1210 helix: 1.73 (0.20), residues: 751 sheet: -0.76 (0.74), residues: 54 loop : -2.07 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 200 HIS 0.003 0.001 HIS C 540 PHE 0.013 0.001 PHE C 267 TYR 0.020 0.001 TYR B 135 ARG 0.003 0.000 ARG C 615 *********************** 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 94 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.990 Fit side-chains REVERT: C 415 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7505 (mtp180) REVERT: B 573 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8756 (ttmm) outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 0.2244 time to fit residues: 28.8948 Evaluate side-chains 86 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 20 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.125340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099970 restraints weight = 12498.417| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.14 r_work: 0.3187 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9553 Z= 0.187 Angle : 0.564 8.156 13073 Z= 0.282 Chirality : 0.040 0.168 1527 Planarity : 0.004 0.043 1627 Dihedral : 4.195 24.214 1345 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.07 % Allowed : 10.50 % Favored : 88.42 % 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: 0.94 (0.26), residues: 1210 helix: 1.95 (0.20), residues: 756 sheet: -0.64 (0.72), residues: 54 loop : -1.90 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 200 HIS 0.005 0.001 HIS C 540 PHE 0.012 0.001 PHE C 267 TYR 0.017 0.001 TYR B 135 ARG 0.003 0.000 ARG B 615 *********************** 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 103 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.959 Fit side-chains REVERT: C 228 TYR cc_start: 0.9324 (p90) cc_final: 0.9086 (p90) REVERT: C 522 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7966 (p0) REVERT: B 573 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8755 (ttmm) outliers start: 10 outliers final: 3 residues processed: 99 average time/residue: 0.2079 time to fit residues: 29.4634 Evaluate side-chains 88 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.123394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098045 restraints weight = 12457.409| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.13 r_work: 0.3155 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9553 Z= 0.258 Angle : 0.587 8.619 13073 Z= 0.291 Chirality : 0.041 0.186 1527 Planarity : 0.005 0.046 1627 Dihedral : 4.230 24.201 1345 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.29 % Allowed : 11.90 % Favored : 86.82 % 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: 0.96 (0.26), residues: 1210 helix: 1.95 (0.20), residues: 755 sheet: -0.55 (0.72), residues: 54 loop : -1.86 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.014 0.001 PHE C 131 TYR 0.024 0.001 TYR B 135 ARG 0.002 0.000 ARG B 138 *********************** 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 96 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.958 Fit side-chains REVERT: C 441 LYS cc_start: 0.8580 (mmmt) cc_final: 0.7922 (mtmt) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 0.2040 time to fit residues: 27.5525 Evaluate side-chains 86 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 57 optimal weight: 0.4980 chunk 95 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.125809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100263 restraints weight = 12341.286| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.16 r_work: 0.3186 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9553 Z= 0.164 Angle : 0.542 7.728 13073 Z= 0.270 Chirality : 0.040 0.194 1527 Planarity : 0.004 0.044 1627 Dihedral : 4.024 23.985 1345 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.86 % Allowed : 12.86 % Favored : 86.28 % 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: 1.24 (0.26), residues: 1210 helix: 2.18 (0.20), residues: 756 sheet: -0.54 (0.72), residues: 54 loop : -1.76 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.011 0.001 PHE B 267 TYR 0.013 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 *********************** 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 100 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.952 Fit side-chains REVERT: C 23 ARG cc_start: 0.7398 (mmm-85) cc_final: 0.6669 (mpp-170) REVERT: C 441 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7992 (ttmt) outliers start: 8 outliers final: 5 residues processed: 97 average time/residue: 0.2165 time to fit residues: 30.0654 Evaluate side-chains 90 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.124821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099195 restraints weight = 12445.762| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.16 r_work: 0.3176 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9553 Z= 0.202 Angle : 0.558 8.104 13073 Z= 0.275 Chirality : 0.040 0.182 1527 Planarity : 0.004 0.047 1627 Dihedral : 3.998 23.882 1345 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.86 % Allowed : 13.29 % Favored : 85.85 % 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: 1.27 (0.26), residues: 1210 helix: 2.18 (0.19), residues: 756 sheet: -0.47 (0.72), residues: 54 loop : -1.72 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.012 0.001 PHE C 131 TYR 0.017 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 *********************** 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 102 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.030 Fit side-chains REVERT: C 23 ARG cc_start: 0.7421 (mmm-85) cc_final: 0.6705 (mpp-170) REVERT: C 441 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8005 (ttmt) REVERT: B 467 ASP cc_start: 0.8337 (m-30) cc_final: 0.8081 (m-30) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.2089 time to fit residues: 29.8138 Evaluate side-chains 94 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 61 optimal weight: 0.0670 chunk 116 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.134464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110032 restraints weight = 12420.232| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.02 r_work: 0.3355 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9553 Z= 0.152 Angle : 0.539 7.540 13073 Z= 0.266 Chirality : 0.039 0.165 1527 Planarity : 0.004 0.049 1627 Dihedral : 3.874 23.767 1345 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.86 % Allowed : 13.83 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.26), residues: 1210 helix: 2.38 (0.19), residues: 753 sheet: -0.45 (0.72), residues: 54 loop : -1.66 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 200 HIS 0.004 0.001 HIS C 540 PHE 0.011 0.001 PHE B 267 TYR 0.010 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 *********************** 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 106 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.067 Fit side-chains REVERT: C 23 ARG cc_start: 0.7346 (mmm-85) cc_final: 0.6622 (mpp-170) REVERT: C 441 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8043 (ttmt) REVERT: B 467 ASP cc_start: 0.8369 (m-30) cc_final: 0.8135 (m-30) outliers start: 8 outliers final: 7 residues processed: 102 average time/residue: 0.2497 time to fit residues: 37.0826 Evaluate side-chains 103 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 303 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 106 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.129612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104788 restraints weight = 12531.534| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.07 r_work: 0.3267 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9553 Z= 0.164 Angle : 0.539 7.698 13073 Z= 0.266 Chirality : 0.040 0.169 1527 Planarity : 0.004 0.051 1627 Dihedral : 3.847 23.790 1345 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.07 % Allowed : 14.04 % Favored : 84.89 % 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: 1.54 (0.26), residues: 1210 helix: 2.42 (0.19), residues: 753 sheet: -0.50 (0.71), residues: 54 loop : -1.61 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 200 HIS 0.004 0.001 HIS C 540 PHE 0.011 0.001 PHE B 267 TYR 0.011 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 *********************** 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 106 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.270 Fit side-chains REVERT: C 23 ARG cc_start: 0.7336 (mmm-85) cc_final: 0.6588 (mpp-170) REVERT: C 441 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8042 (ttmt) REVERT: B 467 ASP cc_start: 0.8375 (m-30) cc_final: 0.8145 (m-30) outliers start: 10 outliers final: 9 residues processed: 100 average time/residue: 0.3175 time to fit residues: 44.5463 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 : 1.223 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 103 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.128841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104039 restraints weight = 12289.008| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.04 r_work: 0.3258 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 0.027 9553 Z= 0.186 Angle : 0.553 7.979 13073 Z= 0.272 Chirality : 0.040 0.180 1527 Planarity : 0.004 0.053 1627 Dihedral : 3.853 23.888 1345 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.18 % Allowed : 14.04 % Favored : 84.78 % 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: 1.54 (0.26), residues: 1210 helix: 2.43 (0.19), residues: 753 sheet: -0.49 (0.71), residues: 54 loop : -1.63 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.011 0.001 PHE B 267 TYR 0.013 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 *********************** 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 105 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.965 Fit side-chains REVERT: C 23 ARG cc_start: 0.7324 (mmm-85) cc_final: 0.6576 (mpp-170) REVERT: C 441 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8059 (ttmt) REVERT: B 467 ASP cc_start: 0.8356 (m-30) cc_final: 0.8129 (m-30) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.2347 time to fit residues: 32.5570 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 : 0.968 ------------------------------------------------------------------------------- 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 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 81 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.129085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104209 restraints weight = 12407.649| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.06 r_work: 0.3260 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9553 Z= 0.178 Angle : 0.547 8.490 13073 Z= 0.270 Chirality : 0.040 0.178 1527 Planarity : 0.004 0.055 1627 Dihedral : 3.842 23.819 1345 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.07 % Allowed : 14.04 % Favored : 84.89 % 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: 1.56 (0.26), residues: 1210 helix: 2.45 (0.19), residues: 753 sheet: -0.67 (0.69), residues: 56 loop : -1.60 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.011 0.001 PHE B 267 TYR 0.013 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 ********************** 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 100 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.998 Fit side-chains REVERT: C 23 ARG cc_start: 0.7311 (mmm-85) cc_final: 0.6576 (mpp-170) REVERT: B 467 ASP cc_start: 0.8369 (m-30) cc_final: 0.8139 (m-30) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.2368 time to fit residues: 31.5174 Evaluate side-chains 98 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.128901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103749 restraints weight = 12349.126| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.11 r_work: 0.3253 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9553 Z= 0.184 Angle : 0.556 8.540 13073 Z= 0.273 Chirality : 0.040 0.180 1527 Planarity : 0.004 0.055 1627 Dihedral : 3.843 23.858 1345 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.07 % Allowed : 14.15 % Favored : 84.78 % 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: 1.57 (0.26), residues: 1210 helix: 2.46 (0.19), residues: 753 sheet: -0.65 (0.69), residues: 56 loop : -1.60 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 200 HIS 0.005 0.001 HIS C 540 PHE 0.011 0.001 PHE B 267 TYR 0.013 0.001 TYR B 135 ARG 0.002 0.000 ARG C 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4776.95 seconds wall clock time: 84 minutes 16.91 seconds (5056.91 seconds total)