Starting phenix.real_space_refine on Wed Aug 5 19:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ylu_39391/08_2026/8ylu_39391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ylu_39391/08_2026/8ylu_39391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ylu_39391/08_2026/8ylu_39391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ylu_39391/08_2026/8ylu_39391.map" model { file = "/net/cci-nas-00/data/ceres_data/8ylu_39391/08_2026/8ylu_39391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ylu_39391/08_2026/8ylu_39391.cif" } resolution = 2.8 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= 0.186 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: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 7175 2.51 5 N 1947 2.21 5 O 2236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11441 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3554 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain: "B" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3554 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1715 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1715 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.88, per 1000 atoms: 0.25 Number of scatterers: 11441 At special positions: 0 Unit cell: (94.64, 118.56, 126.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 44 15.00 Mg 1 11.99 O 2236 8.00 N 1947 7.00 C 7175 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 515.7 milliseconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 46.6% alpha, 12.3% beta 22 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.852A pdb=" N ALA A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.738A pdb=" N GLY A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.549A pdb=" N GLY A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.842A pdb=" N ALA A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.760A pdb=" N ASN A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 161' Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.655A pdb=" N LEU A 251 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.660A pdb=" N ARG A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 365 removed outlier: 4.156A pdb=" N LEU A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.569A pdb=" N LEU A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.704A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.743A pdb=" N ILE A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.646A pdb=" N ALA B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.848A pdb=" N GLY B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.006A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.576A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 319 through 362 removed outlier: 3.873A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.004A pdb=" N SER B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 404 through 426 removed outlier: 3.565A pdb=" N LYS B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 494 through 504 Processing helix chain 'C' and resid 536 through 545 removed outlier: 4.613A pdb=" N ASP C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 561 removed outlier: 3.574A pdb=" N LEU C 561 " --> pdb=" O LEU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 572 Processing helix chain 'C' and resid 583 through 592 removed outlier: 3.510A pdb=" N LEU C 587 " --> pdb=" O ASN C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 604 removed outlier: 3.572A pdb=" N TRP C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.707A pdb=" N ILE D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 504 removed outlier: 5.182A pdb=" N TYR D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Proline residue: D 497 - end of helix Processing helix chain 'D' and resid 506 through 512 removed outlier: 3.950A pdb=" N PHE D 510 " --> pdb=" O TRP D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 removed outlier: 3.583A pdb=" N ALA D 543 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP D 545 " --> pdb=" O GLU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 561 removed outlier: 3.526A pdb=" N LEU D 561 " --> pdb=" O LEU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 595 through 604 removed outlier: 4.125A pdb=" N ARG D 599 " --> pdb=" O ASN D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 5.559A pdb=" N ILE D 515 " --> pdb=" O VAL D 578 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU D 411 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET D 484 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU D 413 " --> pdb=" O MET D 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 223 removed outlier: 5.971A pdb=" N THR A 220 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 308 removed outlier: 4.431A pdb=" N ILE A 305 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 7 removed outlier: 5.579A pdb=" N ILE C 515 " --> pdb=" O VAL C 578 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 481 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL C 518 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE C 483 " --> pdb=" O VAL C 518 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU C 411 " --> pdb=" O ALA C 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'B' and resid 207 through 211 Processing sheet with id=AB2, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.160A pdb=" N THR B 220 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 305 through 308 removed outlier: 4.136A pdb=" N ILE B 305 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 530 through 534 Processing sheet with id=AB5, first strand: chain 'D' and resid 530 through 534 removed outlier: 3.662A pdb=" N SER D 551 " --> pdb=" O HIS D 526 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2990 1.33 - 1.45: 2315 1.45 - 1.57: 6313 1.57 - 1.69: 86 1.69 - 1.81: 70 Bond restraints: 11774 Sorted by residual: bond pdb=" C3' DT F 13 " pdb=" C2' DT F 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC F 17 " pdb=" C2' DC F 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.07e+00 bond pdb=" C3' DT F 5 " pdb=" C2' DT F 5 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.75e+00 bond pdb=" C3' DA E 20 " pdb=" C2' DA E 20 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.76e+00 bond pdb=" C3' DA E 18 " pdb=" O3' DA E 18 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.73e+00 ... (remaining 11769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 15693 1.72 - 3.44: 342 3.44 - 5.16: 23 5.16 - 6.88: 5 6.88 - 8.60: 1 Bond angle restraints: 16064 Sorted by residual: angle pdb=" O4' DA E 10 " pdb=" C4' DA E 10 " pdb=" C3' DA E 10 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.34e+01 angle pdb=" O4' DT F 15 " pdb=" C4' DT F 15 " pdb=" C3' DT F 15 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.28e+01 angle pdb=" O4' DC E 17 " pdb=" C4' DC E 17 " pdb=" C3' DC E 17 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" O4' DA F 18 " pdb=" C4' DA F 18 " pdb=" C3' DA F 18 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT F 3 " pdb=" C4 DT F 3 " pdb=" O4 DT F 3 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 ... (remaining 16059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 6244 28.11 - 56.22: 676 56.22 - 84.33: 58 84.33 - 112.44: 3 112.44 - 140.55: 1 Dihedral angle restraints: 6982 sinusoidal: 3170 harmonic: 3812 Sorted by residual: dihedral pdb=" CA PHE A 36 " pdb=" C PHE A 36 " pdb=" N LYS A 37 " pdb=" CA LYS A 37 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TYR B 238 " pdb=" C TYR B 238 " pdb=" N ASP B 239 " pdb=" CA ASP B 239 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE B 36 " pdb=" C PHE B 36 " pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 6979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1179 0.036 - 0.073: 403 0.073 - 0.109: 111 0.109 - 0.145: 44 0.145 - 0.181: 3 Chirality restraints: 1740 Sorted by residual: chirality pdb=" C3' DA E 16 " pdb=" C4' DA E 16 " pdb=" O3' DA E 16 " pdb=" C2' DA E 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA ASP C 408 " pdb=" N ASP C 408 " pdb=" C ASP C 408 " pdb=" CB ASP C 408 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" C3' DA F 16 " pdb=" C4' DA F 16 " pdb=" O3' DA F 16 " pdb=" C2' DA F 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 1737 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 253 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C ASN B 253 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN B 253 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS B 254 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 14 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C ASN B 14 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN B 14 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU B 15 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 88 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C ALA B 88 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA B 88 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 89 " 0.011 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 345 2.70 - 3.25: 10397 3.25 - 3.80: 18907 3.80 - 4.35: 25437 4.35 - 4.90: 41735 Nonbonded interactions: 96821 Sorted by model distance: nonbonded pdb=" OD1 ASP A 7 " pdb=" OG SER A 10 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR A 117 " pdb=" OP1 DA E 10 " model vdw 2.190 3.040 nonbonded pdb=" N GLU B 284 " pdb=" OE1 GLU B 284 " model vdw 2.212 3.120 nonbonded pdb=" O VAL B 369 " pdb=" NZ LYS B 373 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR B 73 " pdb=" OP2 DA E 8 " model vdw 2.223 3.040 ... (remaining 96816 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 393 through 605) } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11774 Z= 0.256 Angle : 0.554 8.602 16064 Z= 0.405 Chirality : 0.042 0.181 1740 Planarity : 0.003 0.039 1904 Dihedral : 20.360 140.552 4538 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.89 % Allowed : 29.70 % Favored : 69.41 % 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 are not related in a simple way. whole: -0.03 (0.23), residues: 1300 helix: 0.97 (0.23), residues: 548 sheet: -0.44 (0.42), residues: 154 loop : -0.79 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 351 TYR 0.013 0.001 TYR D 575 PHE 0.013 0.001 PHE A 401 TRP 0.011 0.001 TRP C 602 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.26 (11774) covalent geometry : angle 0.55382 / 0.41 (16064) hydrogen bonds : bond 0.12905 / 8.83 ( 517) hydrogen bonds : angle 5.76202 / 4.23 ( 1424) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.372 Fit side-chains REVERT: B 387 MET cc_start: 0.6910 (ttt) cc_final: 0.6666 (tmm) REVERT: D 569 MET cc_start: 0.8847 (ptt) cc_final: 0.8542 (ptt) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.6806 time to fit residues: 94.7667 Evaluate side-chains 123 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 486 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN B 81 GLN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116634 restraints weight = 13287.695| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.52 r_work: 0.3317 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11774 Z= 0.142 Angle : 0.529 8.627 16064 Z= 0.302 Chirality : 0.043 0.206 1740 Planarity : 0.003 0.039 1904 Dihedral : 16.501 142.423 1937 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.10 % Allowed : 26.86 % Favored : 70.04 % 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 are not related in a simple way. whole: -0.11 (0.23), residues: 1300 helix: 1.01 (0.23), residues: 554 sheet: -0.68 (0.40), residues: 164 loop : -0.89 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.013 0.001 TYR D 575 PHE 0.020 0.001 PHE B 401 TRP 0.010 0.001 TRP C 445 HIS 0.003 0.001 HIS D 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (11774) covalent geometry : angle 0.52864 / 0.30 (16064) hydrogen bonds : bond 0.04314 / 2.93 ( 517) hydrogen bonds : angle 4.78516 / 3.48 ( 1424) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.322 Fit side-chains REVERT: A 241 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: A 338 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6291 (ttm170) REVERT: D 512 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8270 (mp10) outliers start: 35 outliers final: 15 residues processed: 152 average time/residue: 0.5763 time to fit residues: 93.9869 Evaluate side-chains 131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116524 restraints weight = 13516.178| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.53 r_work: 0.3318 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11774 Z= 0.139 Angle : 0.516 7.266 16064 Z= 0.295 Chirality : 0.042 0.236 1740 Planarity : 0.003 0.040 1904 Dihedral : 16.498 143.273 1927 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.19 % Allowed : 26.24 % Favored : 70.57 % 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 are not related in a simple way. whole: -0.10 (0.23), residues: 1300 helix: 1.01 (0.23), residues: 556 sheet: -0.64 (0.41), residues: 164 loop : -0.91 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 553 TYR 0.012 0.001 TYR D 575 PHE 0.018 0.001 PHE B 401 TRP 0.011 0.001 TRP C 602 HIS 0.002 0.001 HIS D 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11774) covalent geometry : angle 0.51608 / 0.29 (16064) hydrogen bonds : bond 0.03947 / 2.69 ( 517) hydrogen bonds : angle 4.66237 / 3.38 ( 1424) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.345 Fit side-chains REVERT: A 241 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: A 338 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6274 (ttm170) REVERT: B 124 LYS cc_start: 0.8166 (pttt) cc_final: 0.7862 (pttp) REVERT: B 416 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.5906 (tptp) REVERT: D 512 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8243 (mp10) outliers start: 36 outliers final: 16 residues processed: 143 average time/residue: 0.5639 time to fit residues: 86.5759 Evaluate side-chains 133 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 530 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN B 81 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116719 restraints weight = 13475.992| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.52 r_work: 0.3316 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11774 Z= 0.134 Angle : 0.506 6.727 16064 Z= 0.289 Chirality : 0.042 0.235 1740 Planarity : 0.003 0.042 1904 Dihedral : 16.488 143.624 1927 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.75 % Allowed : 26.77 % Favored : 70.48 % 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 are not related in a simple way. whole: -0.06 (0.23), residues: 1300 helix: 1.05 (0.23), residues: 558 sheet: -0.64 (0.41), residues: 164 loop : -0.90 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 338 TYR 0.013 0.001 TYR D 575 PHE 0.016 0.001 PHE B 401 TRP 0.011 0.001 TRP C 602 HIS 0.002 0.001 HIS D 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11774) covalent geometry : angle 0.50598 / 0.29 (16064) hydrogen bonds : bond 0.03714 / 2.53 ( 517) hydrogen bonds : angle 4.56072 / 3.31 ( 1424) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.301 Fit side-chains REVERT: A 241 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: A 338 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6311 (ttm170) REVERT: B 124 LYS cc_start: 0.8168 (pttt) cc_final: 0.7874 (pttp) REVERT: B 361 LYS cc_start: 0.5815 (OUTLIER) cc_final: 0.5547 (tmtt) REVERT: B 416 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.5917 (tptp) REVERT: C 601 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: D 512 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8169 (mt0) outliers start: 31 outliers final: 14 residues processed: 139 average time/residue: 0.6364 time to fit residues: 95.0019 Evaluate side-chains 136 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 601 GLU Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114852 restraints weight = 13422.346| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.52 r_work: 0.3292 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11774 Z= 0.178 Angle : 0.539 6.888 16064 Z= 0.305 Chirality : 0.044 0.259 1740 Planarity : 0.004 0.044 1904 Dihedral : 16.527 141.837 1926 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.28 % Allowed : 26.33 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1300 helix: 0.97 (0.23), residues: 558 sheet: -0.67 (0.41), residues: 164 loop : -0.95 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.017 0.001 TYR D 575 PHE 0.014 0.001 PHE A 149 TRP 0.012 0.001 TRP C 602 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (11774) covalent geometry : angle 0.53866 / 0.30 (16064) hydrogen bonds : bond 0.04019 / 2.75 ( 517) hydrogen bonds : angle 4.59461 / 3.33 ( 1424) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.501 Fit side-chains REVERT: A 92 ASN cc_start: 0.8112 (t0) cc_final: 0.7873 (t0) REVERT: A 226 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6063 (mpp-170) REVERT: A 241 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: A 338 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6316 (ttm170) REVERT: B 124 LYS cc_start: 0.8111 (pttt) cc_final: 0.7836 (pttp) REVERT: B 361 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5483 (tptp) REVERT: B 416 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5928 (tptp) REVERT: D 512 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8231 (mt0) outliers start: 37 outliers final: 15 residues processed: 153 average time/residue: 0.6991 time to fit residues: 114.5593 Evaluate side-chains 141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 530 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 131 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.0270 chunk 68 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN B 89 ASN B 402 HIS C 605 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116456 restraints weight = 13352.212| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.51 r_work: 0.3316 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11774 Z= 0.128 Angle : 0.509 6.778 16064 Z= 0.290 Chirality : 0.042 0.233 1740 Planarity : 0.003 0.042 1904 Dihedral : 16.482 143.606 1926 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.66 % Allowed : 27.04 % Favored : 70.30 % 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 are not related in a simple way. whole: -0.04 (0.23), residues: 1300 helix: 1.08 (0.23), residues: 558 sheet: -0.41 (0.43), residues: 154 loop : -0.98 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.014 0.001 TYR D 575 PHE 0.014 0.001 PHE A 401 TRP 0.012 0.001 TRP C 602 HIS 0.007 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (11774) covalent geometry : angle 0.50897 / 0.29 (16064) hydrogen bonds : bond 0.03595 / 2.44 ( 517) hydrogen bonds : angle 4.52093 / 3.28 ( 1424) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.516 Fit side-chains REVERT: A 92 ASN cc_start: 0.8066 (t0) cc_final: 0.7835 (t0) REVERT: A 226 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6129 (mpp-170) REVERT: A 241 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: A 338 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6304 (ttm170) REVERT: B 124 LYS cc_start: 0.8117 (pttt) cc_final: 0.7843 (pttp) REVERT: B 361 LYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5534 (tmtt) REVERT: B 416 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.5904 (tptp) REVERT: C 417 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: D 512 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8174 (mp10) outliers start: 30 outliers final: 11 residues processed: 146 average time/residue: 0.6619 time to fit residues: 103.6974 Evaluate side-chains 137 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 113 optimal weight: 0.0060 chunk 89 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117549 restraints weight = 13297.161| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.51 r_work: 0.3331 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11774 Z= 0.120 Angle : 0.500 6.594 16064 Z= 0.285 Chirality : 0.042 0.236 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.439 144.236 1926 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.28 % Allowed : 26.95 % Favored : 69.77 % 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 are not related in a simple way. whole: 0.04 (0.23), residues: 1300 helix: 1.17 (0.23), residues: 558 sheet: -0.37 (0.43), residues: 154 loop : -0.95 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.014 0.001 TYR D 575 PHE 0.014 0.001 PHE A 401 TRP 0.011 0.001 TRP C 602 HIS 0.002 0.000 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (11774) covalent geometry : angle 0.50035 / 0.29 (16064) hydrogen bonds : bond 0.03417 / 2.33 ( 517) hydrogen bonds : angle 4.43221 / 3.21 ( 1424) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.318 Fit side-chains REVERT: A 226 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6121 (mpp-170) REVERT: A 228 GLN cc_start: 0.7839 (mt0) cc_final: 0.7460 (mt0) REVERT: A 241 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: A 324 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7830 (mt) REVERT: A 338 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6336 (ttm170) REVERT: B 124 LYS cc_start: 0.8078 (pttt) cc_final: 0.7806 (pttp) REVERT: B 361 LYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5580 (tmtt) REVERT: B 416 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5813 (tptp) REVERT: C 417 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: D 512 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8161 (mp10) outliers start: 37 outliers final: 12 residues processed: 146 average time/residue: 0.6450 time to fit residues: 100.6712 Evaluate side-chains 140 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 0.0060 chunk 133 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 ASN C 605 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118322 restraints weight = 13315.517| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.51 r_work: 0.3347 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11774 Z= 0.116 Angle : 0.499 6.405 16064 Z= 0.285 Chirality : 0.042 0.237 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.414 144.168 1926 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.48 % Allowed : 27.57 % Favored : 69.95 % 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 are not related in a simple way. whole: 0.10 (0.23), residues: 1300 helix: 1.24 (0.23), residues: 558 sheet: -0.38 (0.43), residues: 154 loop : -0.94 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 351 TYR 0.013 0.001 TYR D 575 PHE 0.017 0.001 PHE B 401 TRP 0.011 0.001 TRP C 602 HIS 0.002 0.000 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (11774) covalent geometry : angle 0.49881 / 0.28 (16064) hydrogen bonds : bond 0.03305 / 2.25 ( 517) hydrogen bonds : angle 4.38601 / 3.18 ( 1424) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.417 Fit side-chains REVERT: A 226 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6134 (mpp-170) REVERT: A 228 GLN cc_start: 0.7809 (mt0) cc_final: 0.7424 (mt0) REVERT: A 241 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: A 338 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6274 (ttm170) REVERT: B 124 LYS cc_start: 0.8121 (pttt) cc_final: 0.7828 (pttp) REVERT: B 361 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5536 (tmtt) REVERT: B 416 LYS cc_start: 0.6382 (OUTLIER) cc_final: 0.5800 (tptp) REVERT: C 417 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: D 512 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8121 (mp10) outliers start: 28 outliers final: 13 residues processed: 141 average time/residue: 0.6936 time to fit residues: 104.6854 Evaluate side-chains 136 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 121 optimal weight: 0.8980 chunk 64 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.0683 > 50:) chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 95 optimal weight: 0.0060 chunk 4 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 ASN B 402 HIS C 595 ASN C 605 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119533 restraints weight = 13221.076| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.51 r_work: 0.3363 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.002 0.030 11774 Z= 0.109 Angle : 0.498 6.241 16064 Z= 0.284 Chirality : 0.041 0.237 1740 Planarity : 0.003 0.040 1904 Dihedral : 16.395 144.637 1926 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 28.19 % Favored : 70.04 % 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 are not related in a simple way. whole: 0.17 (0.23), residues: 1300 helix: 1.33 (0.23), residues: 556 sheet: -0.38 (0.43), residues: 154 loop : -0.92 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.013 0.001 TYR D 575 PHE 0.014 0.001 PHE A 401 TRP 0.010 0.001 TRP C 602 HIS 0.001 0.000 HIS D 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (11774) covalent geometry : angle 0.49774 / 0.28 (16064) hydrogen bonds : bond 0.03187 / 2.18 ( 517) hydrogen bonds : angle 4.33131 / 3.14 ( 1424) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.369 Fit side-chains REVERT: A 226 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6142 (mpp-170) REVERT: A 228 GLN cc_start: 0.7804 (mt0) cc_final: 0.7438 (mt0) REVERT: A 324 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7817 (mt) REVERT: A 338 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6441 (ttm170) REVERT: A 440 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6989 (mp0) REVERT: B 124 LYS cc_start: 0.8160 (pttt) cc_final: 0.7876 (pttp) REVERT: B 361 LYS cc_start: 0.5848 (OUTLIER) cc_final: 0.5507 (tmtt) REVERT: B 416 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5834 (tptp) REVERT: C 417 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: C 601 GLU cc_start: 0.8055 (mp0) cc_final: 0.7853 (mp0) outliers start: 20 outliers final: 12 residues processed: 143 average time/residue: 0.6044 time to fit residues: 92.8628 Evaluate side-chains 140 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN C 595 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118658 restraints weight = 13370.531| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.51 r_work: 0.3354 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.003 0.042 11774 Z= 0.123 Angle : 0.513 6.785 16064 Z= 0.291 Chirality : 0.042 0.239 1740 Planarity : 0.003 0.040 1904 Dihedral : 16.385 143.631 1926 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.60 % Allowed : 28.90 % Favored : 69.50 % 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 are not related in a simple way. whole: 0.16 (0.23), residues: 1300 helix: 1.31 (0.23), residues: 556 sheet: -0.36 (0.43), residues: 154 loop : -0.92 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 300 TYR 0.014 0.001 TYR D 575 PHE 0.014 0.001 PHE B 401 TRP 0.012 0.001 TRP C 602 HIS 0.002 0.000 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11774) covalent geometry : angle 0.51304 / 0.29 (16064) hydrogen bonds : bond 0.03272 / 2.24 ( 517) hydrogen bonds : angle 4.35339 / 3.15 ( 1424) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.414 Fit side-chains REVERT: A 226 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6134 (mpp-170) REVERT: A 228 GLN cc_start: 0.7800 (mt0) cc_final: 0.7438 (mt0) REVERT: A 338 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6439 (ttm170) REVERT: A 440 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7044 (mp0) REVERT: B 124 LYS cc_start: 0.8123 (pttt) cc_final: 0.7846 (pttp) REVERT: B 292 MET cc_start: 0.8831 (mmt) cc_final: 0.8515 (mmt) REVERT: B 361 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5527 (tmtt) REVERT: B 416 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.5828 (tptp) REVERT: C 417 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7800 (m-30) outliers start: 18 outliers final: 13 residues processed: 134 average time/residue: 0.6070 time to fit residues: 87.3861 Evaluate side-chains 139 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN C 595 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116945 restraints weight = 13440.649| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.52 r_work: 0.3321 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11774 Z= 0.144 Angle : 0.533 7.611 16064 Z= 0.300 Chirality : 0.043 0.236 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.386 142.502 1926 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.68 % Allowed : 29.08 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1300 helix: 1.24 (0.23), residues: 556 sheet: -0.40 (0.43), residues: 154 loop : -0.95 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 300 TYR 0.015 0.001 TYR D 575 PHE 0.013 0.001 PHE A 149 TRP 0.012 0.001 TRP C 602 HIS 0.002 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11774) covalent geometry : angle 0.53295 / 0.30 (16064) hydrogen bonds : bond 0.03494 / 2.40 ( 517) hydrogen bonds : angle 4.39576 / 3.18 ( 1424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.27 seconds wall clock time: 59 minutes 24.06 seconds (3564.06 seconds total)