Starting phenix.real_space_refine on Tue Aug 6 12:57:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxf_37905/08_2024/8wxf_37905.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxf_37905/08_2024/8wxf_37905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxf_37905/08_2024/8wxf_37905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxf_37905/08_2024/8wxf_37905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxf_37905/08_2024/8wxf_37905.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxf_37905/08_2024/8wxf_37905.cif" } resolution = 4.0 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 10302 2.51 5 N 2820 2.21 5 O 3210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C GLU 632": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16380 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Chain: "B" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Chain: "C" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Time building chain proxies: 8.94, per 1000 atoms: 0.55 Number of scatterers: 16380 At special positions: 0 Unit cell: (116.16, 113.52, 146.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 3210 8.00 N 2820 7.00 C 10302 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 - 3.50 Amino acid : False - 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: 5.86 Conformation dependent library (CDL) restraints added in 3.0 seconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 21 sheets defined 34.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.645A pdb=" N ALA A 81 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 82 " --> pdb=" O MET A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 82' Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.099A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 254 Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 283 through 293 removed outlier: 4.055A pdb=" N ALA A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.500A pdb=" N GLY A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.220A pdb=" N THR A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 561 through 584 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 617 through 626 Processing helix chain 'A' and resid 643 through 658 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.917A pdb=" N ALA B 82 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 225 through 254 Proline residue: B 238 - end of helix removed outlier: 3.673A pdb=" N ALA B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 283 through 292 removed outlier: 4.024A pdb=" N ALA B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 314 Processing helix chain 'B' and resid 321 through 343 Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.540A pdb=" N GLY B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 561 through 584 Processing helix chain 'B' and resid 606 through 611 removed outlier: 4.488A pdb=" N VAL B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 643 through 659 removed outlier: 3.753A pdb=" N ASN B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.617A pdb=" N ALA C 81 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 82 " --> pdb=" O MET C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 139 through 153 Processing helix chain 'C' and resid 178 through 185 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 225 through 254 Proline residue: C 238 - end of helix Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.528A pdb=" N ILE C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 4.041A pdb=" N ASP C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 344 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.640A pdb=" N THR C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 removed outlier: 3.550A pdb=" N ILE C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.646A pdb=" N GLY C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'C' and resid 561 through 584 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.539A pdb=" N ILE C 607 " --> pdb=" O PRO C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 643 through 658 Processing helix chain 'C' and resid 694 through 699 removed outlier: 4.555A pdb=" N GLY C 699 " --> pdb=" O ILE C 695 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.777A pdb=" N ILE A 17 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 25 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 52 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET A 51 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 124 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 125 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.615A pdb=" N VAL A 190 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 205 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 192 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.921A pdb=" N GLN A 380 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 457 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET A 408 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 460 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 410 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ALA A 462 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.800A pdb=" N ALA A 539 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.869A pdb=" N LEU A 499 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.344A pdb=" N MET B 51 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 124 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 125 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.997A pdb=" N PHE B 187 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 190 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 205 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 192 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 381 through 388 removed outlier: 6.721A pdb=" N MET B 408 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER B 460 " --> pdb=" O MET B 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 498 through 499 Processing sheet with id=AB4, first strand: chain 'B' and resid 539 through 540 removed outlier: 6.834A pdb=" N ALA B 539 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 removed outlier: 5.739A pdb=" N GLU C 5 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 7 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 25 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 17 " --> pdb=" O ARG C 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 7 removed outlier: 5.739A pdb=" N GLU C 5 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 7 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 30 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 52 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET C 51 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 124 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 125 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 172 through 175 removed outlier: 6.718A pdb=" N VAL C 190 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL C 205 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 192 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 380 through 388 removed outlier: 6.174A pdb=" N GLN C 380 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET C 408 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER C 460 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 498 through 500 removed outlier: 3.764A pdb=" N VAL C 519 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 539 through 540 removed outlier: 6.870A pdb=" N ALA C 539 " --> pdb=" O THR C 546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 629 through 631 removed outlier: 3.633A pdb=" N PHE C 638 " --> pdb=" O SER C 630 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 723 through 724 removed outlier: 4.114A pdb=" N ASP C 723 " --> pdb=" O SER C 731 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 731 " --> pdb=" O ASP C 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 657 hydrogen bonds defined for protein. 1878 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: 5.30 Time building geometry restraints manager: 6.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5634 1.34 - 1.46: 3225 1.46 - 1.58: 7680 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 16626 Sorted by residual: bond pdb=" N VAL B 278 " pdb=" CA VAL B 278 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.19e+00 bond pdb=" N GLU C 77 " pdb=" CA GLU C 77 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.52e+00 bond pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.23e-02 6.61e+03 6.52e+00 bond pdb=" N LEU C 313 " pdb=" CA LEU C 313 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.17e+00 bond pdb=" N MET C 497 " pdb=" CA MET C 497 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.07e+00 ... (remaining 16621 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.27: 259 104.27 - 111.70: 7748 111.70 - 119.14: 5953 119.14 - 126.57: 8478 126.57 - 134.00: 128 Bond angle restraints: 22566 Sorted by residual: angle pdb=" N VAL C 186 " pdb=" CA VAL C 186 " pdb=" C VAL C 186 " ideal model delta sigma weight residual 113.47 108.80 4.67 1.01e+00 9.80e-01 2.14e+01 angle pdb=" N VAL A 510 " pdb=" CA VAL A 510 " pdb=" C VAL A 510 " ideal model delta sigma weight residual 113.71 109.59 4.12 9.50e-01 1.11e+00 1.88e+01 angle pdb=" N ASP C 47 " pdb=" CA ASP C 47 " pdb=" C ASP C 47 " ideal model delta sigma weight residual 112.86 107.89 4.97 1.22e+00 6.72e-01 1.66e+01 angle pdb=" CA GLU A 515 " pdb=" CB GLU A 515 " pdb=" CG GLU A 515 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLN A 311 " pdb=" CB GLN A 311 " pdb=" CG GLN A 311 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.37e+01 ... (remaining 22561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8590 17.48 - 34.97: 1139 34.97 - 52.45: 290 52.45 - 69.93: 51 69.93 - 87.42: 34 Dihedral angle restraints: 10104 sinusoidal: 3918 harmonic: 6186 Sorted by residual: dihedral pdb=" CA GLU B 515 " pdb=" C GLU B 515 " pdb=" N ARG B 516 " pdb=" CA ARG B 516 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU A 554 " pdb=" C LEU A 554 " pdb=" N ASP A 555 " pdb=" CA ASP A 555 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 524 " pdb=" C ILE B 524 " pdb=" N LEU B 525 " pdb=" CA LEU B 525 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 10101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1995 0.047 - 0.095: 502 0.095 - 0.142: 169 0.142 - 0.189: 8 0.189 - 0.236: 2 Chirality restraints: 2676 Sorted by residual: chirality pdb=" CB VAL B 561 " pdb=" CA VAL B 561 " pdb=" CG1 VAL B 561 " pdb=" CG2 VAL B 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL A 561 " pdb=" CA VAL A 561 " pdb=" CG1 VAL A 561 " pdb=" CG2 VAL A 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL B 278 " pdb=" N VAL B 278 " pdb=" C VAL B 278 " pdb=" CB VAL B 278 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 2673 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 557 " 0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO B 558 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 558 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 558 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 267 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO B 268 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 47 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" CG ASP B 47 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP B 47 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP B 47 " 0.019 2.00e-02 2.50e+03 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1107 2.73 - 3.27: 17011 3.27 - 3.82: 25895 3.82 - 4.36: 28346 4.36 - 4.90: 48783 Nonbonded interactions: 121142 Sorted by model distance: nonbonded pdb=" O ASP A 343 " pdb=" ND1 HIS A 344 " model vdw 2.188 3.120 nonbonded pdb=" O ASN A 655 " pdb=" NE2 GLN A 661 " model vdw 2.224 3.120 nonbonded pdb=" O ALA B 287 " pdb=" OG1 THR B 291 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG C 356 " pdb=" OD2 ASP C 523 " model vdw 2.239 3.120 nonbonded pdb=" NH1 ARG C 350 " pdb=" O GLY C 351 " model vdw 2.243 3.120 ... (remaining 121137 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' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 43.280 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.003 0.045 16626 Z= 0.218 Angle : 0.709 10.247 22566 Z= 0.386 Chirality : 0.046 0.236 2676 Planarity : 0.005 0.087 2979 Dihedral : 17.293 87.415 6138 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 0.75 % Allowed : 33.16 % Favored : 66.09 % 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: -1.25 (0.18), residues: 2184 helix: 0.61 (0.20), residues: 693 sheet: -1.44 (0.31), residues: 325 loop : -1.55 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 173 HIS 0.003 0.001 HIS B 409 PHE 0.014 0.001 PHE C 531 TYR 0.010 0.001 TYR B 276 ARG 0.008 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ASP cc_start: 0.9054 (m-30) cc_final: 0.8764 (p0) REVERT: A 333 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8944 (tttt) REVERT: A 337 ARG cc_start: 0.9115 (mtp85) cc_final: 0.8662 (mtp85) REVERT: B 328 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9277 (mt) REVERT: C 208 GLU cc_start: 0.6663 (tp30) cc_final: 0.6335 (tp30) REVERT: C 249 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8224 (mt-10) REVERT: C 482 LEU cc_start: 0.8746 (mm) cc_final: 0.8314 (mm) REVERT: C 495 ILE cc_start: 0.8605 (mp) cc_final: 0.8190 (mm) REVERT: C 534 MET cc_start: 0.7696 (tpt) cc_final: 0.7452 (tpp) outliers start: 13 outliers final: 4 residues processed: 199 average time/residue: 0.2493 time to fit residues: 77.2859 Evaluate side-chains 184 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16626 Z= 0.202 Angle : 0.601 10.291 22566 Z= 0.310 Chirality : 0.044 0.201 2676 Planarity : 0.005 0.060 2979 Dihedral : 4.694 55.625 2357 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.73 % Rotamer: Outliers : 4.44 % Allowed : 28.09 % Favored : 67.47 % 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: -0.92 (0.18), residues: 2184 helix: 0.88 (0.20), residues: 697 sheet: -1.21 (0.30), residues: 329 loop : -1.37 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 173 HIS 0.002 0.000 HIS C 694 PHE 0.018 0.001 PHE A 531 TYR 0.012 0.001 TYR B 270 ARG 0.004 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 188 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8903 (tttt) REVERT: A 345 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8580 (p90) REVERT: A 482 LEU cc_start: 0.9022 (mm) cc_final: 0.8518 (mm) REVERT: A 522 THR cc_start: 0.9128 (m) cc_final: 0.8570 (p) REVERT: B 47 ASP cc_start: 0.8089 (t0) cc_final: 0.7885 (t0) REVERT: B 328 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9272 (mt) REVERT: B 389 MET cc_start: 0.8260 (mmm) cc_final: 0.7875 (mtt) REVERT: C 79 MET cc_start: 0.8430 (tpp) cc_final: 0.8200 (tpp) REVERT: C 215 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8651 (pp20) REVERT: C 482 LEU cc_start: 0.8655 (mm) cc_final: 0.8230 (mm) outliers start: 77 outliers final: 36 residues processed: 244 average time/residue: 0.2293 time to fit residues: 89.4540 Evaluate side-chains 208 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 215 optimal weight: 0.0370 chunk 177 optimal weight: 20.0000 chunk 197 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16626 Z= 0.163 Angle : 0.565 11.929 22566 Z= 0.286 Chirality : 0.043 0.165 2676 Planarity : 0.004 0.051 2979 Dihedral : 4.467 53.223 2356 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 4.27 % Allowed : 28.43 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.19), residues: 2184 helix: 1.01 (0.20), residues: 699 sheet: -1.12 (0.30), residues: 329 loop : -1.21 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 173 HIS 0.002 0.000 HIS A 344 PHE 0.023 0.001 PHE B 345 TYR 0.012 0.001 TYR A 276 ARG 0.013 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 188 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 333 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8921 (tttt) REVERT: A 345 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8545 (p90) REVERT: A 482 LEU cc_start: 0.9037 (mm) cc_final: 0.8524 (mm) REVERT: A 522 THR cc_start: 0.9168 (m) cc_final: 0.8594 (p) REVERT: B 30 GLU cc_start: 0.8324 (pt0) cc_final: 0.7549 (pm20) REVERT: B 47 ASP cc_start: 0.8092 (t0) cc_final: 0.7830 (t0) REVERT: B 204 MET cc_start: 0.8811 (tmm) cc_final: 0.8510 (tmm) REVERT: B 328 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9257 (mt) REVERT: B 389 MET cc_start: 0.8342 (mmm) cc_final: 0.7894 (mtt) REVERT: B 497 MET cc_start: 0.7838 (mmt) cc_final: 0.7524 (mmm) REVERT: C 30 GLU cc_start: 0.8377 (tt0) cc_final: 0.7508 (mt-10) REVERT: C 204 MET cc_start: 0.8869 (tmm) cc_final: 0.8570 (tmm) REVERT: C 215 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8662 (pp20) REVERT: C 320 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6908 (mtm-85) outliers start: 74 outliers final: 40 residues processed: 242 average time/residue: 0.2304 time to fit residues: 88.5753 Evaluate side-chains 220 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 0.1980 chunk 149 optimal weight: 7.9990 chunk 103 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 199 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16626 Z= 0.176 Angle : 0.554 12.303 22566 Z= 0.280 Chirality : 0.044 0.328 2676 Planarity : 0.004 0.052 2979 Dihedral : 4.359 52.396 2356 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 4.33 % Allowed : 28.26 % Favored : 67.42 % 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: -0.63 (0.18), residues: 2184 helix: 1.08 (0.20), residues: 701 sheet: -1.12 (0.29), residues: 329 loop : -1.14 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.012 0.001 TYR C 454 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 178 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8994 (mm-40) REVERT: A 333 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8950 (ttpt) REVERT: A 522 THR cc_start: 0.9128 (m) cc_final: 0.8550 (p) REVERT: B 30 GLU cc_start: 0.8341 (pt0) cc_final: 0.7540 (pm20) REVERT: B 47 ASP cc_start: 0.8155 (t0) cc_final: 0.7897 (t0) REVERT: B 51 MET cc_start: 0.8406 (ttt) cc_final: 0.8028 (ttt) REVERT: B 189 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7713 (mtp) REVERT: B 204 MET cc_start: 0.8672 (tmm) cc_final: 0.8468 (tmm) REVERT: B 328 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9263 (mt) REVERT: B 389 MET cc_start: 0.8449 (mmm) cc_final: 0.7991 (mtt) REVERT: B 590 MET cc_start: 0.6036 (tpp) cc_final: 0.5751 (tpp) REVERT: C 30 GLU cc_start: 0.8367 (tt0) cc_final: 0.7512 (mt-10) REVERT: C 204 MET cc_start: 0.8891 (tmm) cc_final: 0.8606 (tmm) REVERT: C 215 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8710 (pp20) REVERT: C 320 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6980 (mtm-85) REVERT: C 497 MET cc_start: 0.7591 (mmt) cc_final: 0.7384 (mmm) outliers start: 75 outliers final: 50 residues processed: 235 average time/residue: 0.2297 time to fit residues: 86.8338 Evaluate side-chains 226 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 172 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS A 412 ASN B 65 HIS B 412 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 412 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16626 Z= 0.362 Angle : 0.650 12.112 22566 Z= 0.331 Chirality : 0.046 0.285 2676 Planarity : 0.005 0.060 2979 Dihedral : 4.618 52.332 2356 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.77 % Favored : 94.09 % Rotamer: Outliers : 5.71 % Allowed : 28.03 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2184 helix: 0.99 (0.20), residues: 708 sheet: -1.35 (0.28), residues: 329 loop : -1.26 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 173 HIS 0.004 0.001 HIS C 409 PHE 0.029 0.002 PHE A 345 TYR 0.018 0.002 TYR A 80 ARG 0.005 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 169 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8970 (ttpt) REVERT: A 643 ASP cc_start: 0.8580 (t70) cc_final: 0.8241 (t70) REVERT: B 47 ASP cc_start: 0.8279 (t0) cc_final: 0.7994 (t0) REVERT: B 51 MET cc_start: 0.8366 (ttt) cc_final: 0.8081 (ttt) REVERT: B 328 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9309 (mt) REVERT: B 389 MET cc_start: 0.8607 (mmm) cc_final: 0.8191 (mtt) REVERT: B 412 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8233 (m-40) REVERT: C 30 GLU cc_start: 0.8348 (tt0) cc_final: 0.7507 (mt-10) REVERT: C 79 MET cc_start: 0.9184 (tmm) cc_final: 0.8812 (tpp) REVERT: C 215 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8760 (pp20) REVERT: C 320 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7075 (mtm-85) outliers start: 99 outliers final: 66 residues processed: 246 average time/residue: 0.2267 time to fit residues: 90.3556 Evaluate side-chains 231 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 161 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 694 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 0.0170 chunk 190 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 308 GLN B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16626 Z= 0.205 Angle : 0.591 13.224 22566 Z= 0.294 Chirality : 0.045 0.310 2676 Planarity : 0.005 0.054 2979 Dihedral : 4.465 51.918 2356 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.76 % Favored : 95.10 % Rotamer: Outliers : 4.67 % Allowed : 29.58 % Favored : 65.74 % 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: -0.67 (0.18), residues: 2184 helix: 1.04 (0.20), residues: 708 sheet: -1.21 (0.29), residues: 327 loop : -1.16 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 173 HIS 0.005 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.011 0.001 TYR B 411 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 176 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8954 (ttpt) REVERT: A 643 ASP cc_start: 0.8601 (t70) cc_final: 0.8233 (t70) REVERT: B 47 ASP cc_start: 0.8248 (t0) cc_final: 0.7964 (t0) REVERT: B 204 MET cc_start: 0.8769 (tmm) cc_final: 0.8550 (tmm) REVERT: B 328 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9338 (mt) REVERT: B 389 MET cc_start: 0.8601 (mmm) cc_final: 0.8058 (mtt) REVERT: C 30 GLU cc_start: 0.8348 (tt0) cc_final: 0.7487 (mt-10) REVERT: C 79 MET cc_start: 0.9240 (mmm) cc_final: 0.8849 (tpp) REVERT: C 181 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: C 204 MET cc_start: 0.8823 (tmm) cc_final: 0.8595 (tmm) REVERT: C 215 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8773 (pp20) REVERT: C 320 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6712 (mtm180) outliers start: 81 outliers final: 63 residues processed: 241 average time/residue: 0.2221 time to fit residues: 86.6135 Evaluate side-chains 236 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 169 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 694 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16626 Z= 0.178 Angle : 0.588 12.773 22566 Z= 0.287 Chirality : 0.044 0.286 2676 Planarity : 0.004 0.054 2979 Dihedral : 4.189 50.929 2353 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Rotamer: Outliers : 4.33 % Allowed : 29.82 % Favored : 65.86 % 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: -0.59 (0.18), residues: 2184 helix: 1.09 (0.20), residues: 707 sheet: -1.19 (0.29), residues: 337 loop : -1.07 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 173 HIS 0.004 0.000 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.010 0.001 TYR B 411 ARG 0.003 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 174 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.9061 (tmm) cc_final: 0.8739 (tmm) REVERT: A 303 ASP cc_start: 0.9101 (m-30) cc_final: 0.8864 (p0) REVERT: A 412 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7893 (m110) REVERT: A 643 ASP cc_start: 0.8471 (t70) cc_final: 0.8092 (t70) REVERT: B 47 ASP cc_start: 0.8258 (t0) cc_final: 0.7998 (t0) REVERT: B 189 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7720 (mtm) REVERT: B 204 MET cc_start: 0.8786 (tmm) cc_final: 0.8554 (tmm) REVERT: B 208 GLU cc_start: 0.7190 (tp30) cc_final: 0.6919 (tp30) REVERT: B 590 MET cc_start: 0.5909 (tpp) cc_final: 0.5505 (tpp) REVERT: C 30 GLU cc_start: 0.8306 (tt0) cc_final: 0.7432 (mt-10) REVERT: C 79 MET cc_start: 0.9253 (mmm) cc_final: 0.8872 (tpp) REVERT: C 181 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: C 204 MET cc_start: 0.8856 (tmm) cc_final: 0.8621 (tmm) REVERT: C 215 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8737 (pp20) REVERT: C 320 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6870 (mtm-85) REVERT: C 497 MET cc_start: 0.8483 (mmm) cc_final: 0.8275 (mmm) outliers start: 75 outliers final: 59 residues processed: 237 average time/residue: 0.2244 time to fit residues: 85.8780 Evaluate side-chains 233 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 169 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 50.0000 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 65 HIS ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16626 Z= 0.302 Angle : 0.641 12.909 22566 Z= 0.319 Chirality : 0.045 0.259 2676 Planarity : 0.005 0.064 2979 Dihedral : 4.154 50.961 2350 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.54 % Favored : 94.32 % Rotamer: Outliers : 4.84 % Allowed : 29.30 % Favored : 65.86 % 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: -0.69 (0.18), residues: 2184 helix: 1.08 (0.20), residues: 709 sheet: -1.43 (0.28), residues: 339 loop : -1.13 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.005 0.001 HIS B 409 PHE 0.022 0.002 PHE A 531 TYR 0.016 0.002 TYR B 80 ARG 0.006 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 164 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.7999 (t0) REVERT: A 643 ASP cc_start: 0.8658 (t70) cc_final: 0.8274 (t70) REVERT: B 47 ASP cc_start: 0.8308 (t0) cc_final: 0.8034 (t0) REVERT: B 51 MET cc_start: 0.8373 (ttt) cc_final: 0.8000 (ttt) REVERT: B 189 MET cc_start: 0.8157 (mtp) cc_final: 0.7777 (mtm) REVERT: B 204 MET cc_start: 0.8863 (tmm) cc_final: 0.8585 (tmm) REVERT: B 389 MET cc_start: 0.8767 (mmm) cc_final: 0.8001 (mtt) REVERT: B 590 MET cc_start: 0.6151 (tpp) cc_final: 0.5889 (tpp) REVERT: B 693 VAL cc_start: 0.4455 (OUTLIER) cc_final: 0.4165 (t) REVERT: C 30 GLU cc_start: 0.8318 (tt0) cc_final: 0.7468 (mt-10) REVERT: C 79 MET cc_start: 0.9275 (mmm) cc_final: 0.8876 (tpp) REVERT: C 181 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: C 204 MET cc_start: 0.8899 (tmm) cc_final: 0.8588 (tmm) REVERT: C 215 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8776 (pp20) REVERT: C 320 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7057 (mtm-85) outliers start: 84 outliers final: 67 residues processed: 230 average time/residue: 0.2368 time to fit residues: 86.5408 Evaluate side-chains 231 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 159 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 184 optimal weight: 0.6980 chunk 196 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16626 Z= 0.180 Angle : 0.609 12.730 22566 Z= 0.297 Chirality : 0.044 0.205 2676 Planarity : 0.004 0.062 2979 Dihedral : 4.019 50.800 2350 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.35 % Favored : 95.51 % Rotamer: Outliers : 4.15 % Allowed : 30.10 % Favored : 65.74 % 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: -0.59 (0.18), residues: 2184 helix: 1.11 (0.20), residues: 707 sheet: -1.27 (0.28), residues: 337 loop : -1.06 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 173 HIS 0.005 0.001 HIS A 344 PHE 0.021 0.001 PHE A 531 TYR 0.009 0.001 TYR B 276 ARG 0.003 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 174 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.9054 (tmm) cc_final: 0.8817 (tmm) REVERT: A 303 ASP cc_start: 0.9125 (m-30) cc_final: 0.8893 (p0) REVERT: A 318 GLU cc_start: 0.7760 (mp0) cc_final: 0.7265 (mp0) REVERT: A 555 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.7933 (t0) REVERT: A 643 ASP cc_start: 0.8511 (t70) cc_final: 0.8125 (t70) REVERT: B 47 ASP cc_start: 0.8279 (t0) cc_final: 0.8019 (t0) REVERT: B 189 MET cc_start: 0.8039 (mtp) cc_final: 0.7728 (mtm) REVERT: B 204 MET cc_start: 0.8760 (tmm) cc_final: 0.8524 (tmm) REVERT: B 208 GLU cc_start: 0.7150 (tp30) cc_final: 0.6668 (tp30) REVERT: B 389 MET cc_start: 0.8724 (mmm) cc_final: 0.7381 (mmm) REVERT: B 590 MET cc_start: 0.6163 (tpp) cc_final: 0.5863 (tpp) REVERT: B 693 VAL cc_start: 0.4431 (OUTLIER) cc_final: 0.4144 (t) REVERT: C 30 GLU cc_start: 0.8346 (tt0) cc_final: 0.7451 (mt-10) REVERT: C 79 MET cc_start: 0.9253 (mmm) cc_final: 0.8899 (tpp) REVERT: C 181 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: C 204 MET cc_start: 0.8839 (tmm) cc_final: 0.8589 (tmm) REVERT: C 215 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8758 (pp20) REVERT: C 320 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7001 (mpp80) outliers start: 72 outliers final: 62 residues processed: 236 average time/residue: 0.2310 time to fit residues: 88.5189 Evaluate side-chains 235 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 168 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 5.9990 chunk 126 optimal weight: 0.0170 chunk 98 optimal weight: 6.9990 chunk 144 optimal weight: 0.0980 chunk 218 optimal weight: 8.9990 chunk 200 optimal weight: 0.0980 chunk 173 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16626 Z= 0.171 Angle : 0.606 12.840 22566 Z= 0.294 Chirality : 0.044 0.213 2676 Planarity : 0.004 0.063 2979 Dihedral : 3.926 50.120 2350 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 3.75 % Allowed : 30.57 % Favored : 65.69 % 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: -0.50 (0.19), residues: 2184 helix: 1.13 (0.20), residues: 707 sheet: -1.18 (0.29), residues: 337 loop : -0.98 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 173 HIS 0.004 0.000 HIS A 344 PHE 0.024 0.001 PHE A 531 TYR 0.014 0.001 TYR C 276 ARG 0.002 0.000 ARG A 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 180 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.9067 (tmm) cc_final: 0.8836 (tmm) REVERT: A 303 ASP cc_start: 0.9126 (m-30) cc_final: 0.8919 (p0) REVERT: A 318 GLU cc_start: 0.7739 (mp0) cc_final: 0.7260 (mp0) REVERT: A 643 ASP cc_start: 0.8493 (t70) cc_final: 0.8095 (t70) REVERT: B 189 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7713 (mtm) REVERT: B 204 MET cc_start: 0.8816 (tmm) cc_final: 0.8592 (tmm) REVERT: B 208 GLU cc_start: 0.6961 (tp30) cc_final: 0.6505 (tp30) REVERT: B 388 ASP cc_start: 0.8684 (t0) cc_final: 0.8231 (t0) REVERT: B 389 MET cc_start: 0.8727 (mmm) cc_final: 0.7482 (mmm) REVERT: B 590 MET cc_start: 0.6114 (tpp) cc_final: 0.5833 (tpp) REVERT: B 693 VAL cc_start: 0.4450 (OUTLIER) cc_final: 0.4155 (t) REVERT: C 30 GLU cc_start: 0.8306 (tt0) cc_final: 0.7405 (mt-10) REVERT: C 79 MET cc_start: 0.9254 (mmm) cc_final: 0.8872 (tpp) REVERT: C 181 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8340 (pm20) REVERT: C 204 MET cc_start: 0.8853 (tmm) cc_final: 0.8595 (tmm) REVERT: C 215 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8753 (pp20) REVERT: C 313 LEU cc_start: 0.8768 (mp) cc_final: 0.8228 (tt) REVERT: C 320 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6938 (mpp80) outliers start: 65 outliers final: 58 residues processed: 234 average time/residue: 0.2391 time to fit residues: 90.3942 Evaluate side-chains 236 residues out of total 1734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 0.0570 chunk 174 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.149389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108796 restraints weight = 30994.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106874 restraints weight = 22593.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107967 restraints weight = 19369.296| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16626 Z= 0.178 Angle : 0.606 12.129 22566 Z= 0.296 Chirality : 0.044 0.201 2676 Planarity : 0.004 0.060 2979 Dihedral : 3.891 49.307 2350 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 3.86 % Allowed : 30.51 % Favored : 65.63 % 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: -0.45 (0.19), residues: 2184 helix: 1.17 (0.20), residues: 707 sheet: -1.15 (0.29), residues: 337 loop : -0.94 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 173 HIS 0.004 0.001 HIS A 344 PHE 0.023 0.001 PHE A 531 TYR 0.009 0.001 TYR C 138 ARG 0.002 0.000 ARG C 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.69 seconds wall clock time: 55 minutes 57.77 seconds (3357.77 seconds total)