Starting phenix.real_space_refine on Tue Feb 11 12:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dcr_30640/02_2025/7dcr_30640.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dcr_30640/02_2025/7dcr_30640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dcr_30640/02_2025/7dcr_30640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dcr_30640/02_2025/7dcr_30640.map" model { file = "/net/cci-nas-00/data/ceres_data/7dcr_30640/02_2025/7dcr_30640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dcr_30640/02_2025/7dcr_30640.cif" } resolution = 3.15 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 55 atoms to isotropic. 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 35 5.16 5 C 3613 2.51 5 N 964 2.21 5 O 1041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5653 Number of models: 1 Model: "" Number of chains: 2 Chain: "x" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5197 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 619} Chain: "y" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 456 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.99, per 1000 atoms: 0.71 Number of scatterers: 5653 At special positions: 0 Unit cell: (86.7875, 88.1125, 80.825, 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 35 16.00 O 1041 8.00 N 964 7.00 C 3613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 686.8 milliseconds 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 45.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'x' and resid 228 through 237 removed outlier: 3.526A pdb=" N LEU x 232 " --> pdb=" O TYR x 228 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU x 235 " --> pdb=" O GLU x 231 " (cutoff:3.500A) Processing helix chain 'x' and resid 255 through 264 removed outlier: 3.514A pdb=" N VAL x 261 " --> pdb=" O PRO x 257 " (cutoff:3.500A) Processing helix chain 'x' and resid 279 through 295 removed outlier: 3.686A pdb=" N THR x 284 " --> pdb=" O ARG x 280 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL x 286 " --> pdb=" O ALA x 282 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN x 295 " --> pdb=" O ALA x 291 " (cutoff:3.500A) Processing helix chain 'x' and resid 323 through 329 removed outlier: 3.719A pdb=" N LEU x 327 " --> pdb=" O THR x 323 " (cutoff:3.500A) Processing helix chain 'x' and resid 330 through 332 No H-bonds generated for 'chain 'x' and resid 330 through 332' Processing helix chain 'x' and resid 347 through 351 Processing helix chain 'x' and resid 352 through 357 Processing helix chain 'x' and resid 357 through 365 removed outlier: 3.505A pdb=" N ASP x 364 " --> pdb=" O GLY x 360 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE x 365 " --> pdb=" O LEU x 361 " (cutoff:3.500A) Processing helix chain 'x' and resid 382 through 390 removed outlier: 3.523A pdb=" N SER x 387 " --> pdb=" O ALA x 383 " (cutoff:3.500A) Processing helix chain 'x' and resid 418 through 431 removed outlier: 3.547A pdb=" N ILE x 425 " --> pdb=" O ALA x 421 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR x 431 " --> pdb=" O GLN x 427 " (cutoff:3.500A) Processing helix chain 'x' and resid 444 through 463 removed outlier: 3.535A pdb=" N LYS x 454 " --> pdb=" O ARG x 450 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET x 459 " --> pdb=" O LEU x 455 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU x 462 " --> pdb=" O ILE x 458 " (cutoff:3.500A) Processing helix chain 'x' and resid 479 through 488 removed outlier: 4.082A pdb=" N LYS x 485 " --> pdb=" O GLU x 481 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE x 486 " --> pdb=" O GLN x 482 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE x 487 " --> pdb=" O GLN x 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN x 488 " --> pdb=" O LEU x 484 " (cutoff:3.500A) Processing helix chain 'x' and resid 542 through 551 Processing helix chain 'x' and resid 566 through 573 Processing helix chain 'x' and resid 587 through 597 removed outlier: 3.519A pdb=" N LEU x 592 " --> pdb=" O SER x 588 " (cutoff:3.500A) Processing helix chain 'x' and resid 612 through 626 removed outlier: 3.572A pdb=" N LYS x 618 " --> pdb=" O PRO x 614 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER x 619 " --> pdb=" O THR x 615 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU x 623 " --> pdb=" O SER x 619 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE x 625 " --> pdb=" O GLU x 621 " (cutoff:3.500A) Processing helix chain 'x' and resid 636 through 643 removed outlier: 3.625A pdb=" N CYS x 643 " --> pdb=" O GLY x 639 " (cutoff:3.500A) Processing helix chain 'x' and resid 650 through 661 removed outlier: 3.585A pdb=" N VAL x 654 " --> pdb=" O GLU x 650 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA x 659 " --> pdb=" O LEU x 655 " (cutoff:3.500A) Processing helix chain 'x' and resid 667 through 679 removed outlier: 3.915A pdb=" N THR x 673 " --> pdb=" O GLU x 669 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE x 674 " --> pdb=" O GLU x 670 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER x 676 " --> pdb=" O LEU x 672 " (cutoff:3.500A) Processing helix chain 'x' and resid 688 through 697 removed outlier: 3.785A pdb=" N ALA x 692 " --> pdb=" O GLN x 688 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA x 694 " --> pdb=" O ARG x 690 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER x 695 " --> pdb=" O ASP x 691 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL x 696 " --> pdb=" O ALA x 692 " (cutoff:3.500A) Processing helix chain 'x' and resid 702 through 717 removed outlier: 3.584A pdb=" N TYR x 707 " --> pdb=" O ASP x 703 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE x 711 " --> pdb=" O TYR x 707 " (cutoff:3.500A) Processing helix chain 'x' and resid 720 through 727 removed outlier: 3.795A pdb=" N CYS x 724 " --> pdb=" O SER x 720 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN x 725 " --> pdb=" O ARG x 721 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP x 726 " --> pdb=" O SER x 722 " (cutoff:3.500A) Processing helix chain 'x' and resid 730 through 752 removed outlier: 3.608A pdb=" N MET x 734 " --> pdb=" O GLN x 730 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG x 736 " --> pdb=" O LYS x 732 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS x 750 " --> pdb=" O ARG x 746 " (cutoff:3.500A) Processing helix chain 'x' and resid 754 through 764 removed outlier: 3.523A pdb=" N ALA x 760 " --> pdb=" O LYS x 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE x 764 " --> pdb=" O ALA x 760 " (cutoff:3.500A) Processing helix chain 'x' and resid 767 through 781 removed outlier: 3.520A pdb=" N ILE x 771 " --> pdb=" O ILE x 767 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN x 772 " --> pdb=" O ALA x 768 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA x 773 " --> pdb=" O GLY x 769 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR x 776 " --> pdb=" O ASN x 772 " (cutoff:3.500A) Processing helix chain 'x' and resid 813 through 821 removed outlier: 3.866A pdb=" N VAL x 817 " --> pdb=" O SER x 813 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS x 819 " --> pdb=" O LEU x 815 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS x 820 " --> pdb=" O PHE x 816 " (cutoff:3.500A) Processing helix chain 'x' and resid 852 through 857 Processing helix chain 'x' and resid 859 through 867 removed outlier: 3.570A pdb=" N PHE x 863 " --> pdb=" O VAL x 859 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP x 865 " --> pdb=" O GLN x 861 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU x 866 " --> pdb=" O ILE x 862 " (cutoff:3.500A) Processing helix chain 'y' and resid 95 through 100 Processing helix chain 'y' and resid 101 through 111 removed outlier: 3.808A pdb=" N ASP y 107 " --> pdb=" O GLU y 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU y 110 " --> pdb=" O GLY y 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG y 111 " --> pdb=" O ASP y 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 310 through 311 removed outlier: 3.593A pdb=" N TYR x 304 " --> pdb=" O LYS x 311 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY x 303 " --> pdb=" O TYR x 321 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE x 273 " --> pdb=" O LYS x 320 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET x 322 " --> pdb=" O ILE x 273 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE x 275 " --> pdb=" O MET x 322 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN x 272 " --> pdb=" O TYR x 340 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS x 342 " --> pdb=" O GLN x 272 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER x 341 " --> pdb=" O LYS x 373 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU x 375 " --> pdb=" O SER x 341 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE x 343 " --> pdb=" O LEU x 375 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER x 377 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE x 345 " --> pdb=" O SER x 377 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N PHE x 396 " --> pdb=" O VAL x 241 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE x 243 " --> pdb=" O PHE x 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 406 through 409 removed outlier: 7.074A pdb=" N ARG x 514 " --> pdb=" O LYS x 560 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE x 562 " --> pdb=" O ARG x 514 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL x 516 " --> pdb=" O PHE x 562 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP x 437 " --> pdb=" O TYR x 515 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE x 517 " --> pdb=" O ASP x 437 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU x 439 " --> pdb=" O ILE x 517 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE x 438 " --> pdb=" O VAL x 498 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA x 500 " --> pdb=" O ILE x 438 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL x 440 " --> pdb=" O ALA x 500 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN x 468 " --> pdb=" O ARG x 495 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL x 497 " --> pdb=" O GLN x 468 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE x 470 " --> pdb=" O VAL x 497 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU x 499 " --> pdb=" O ILE x 470 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR x 472 " --> pdb=" O LEU x 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 521 through 527 removed outlier: 5.421A pdb=" N LEU x 835 " --> pdb=" O THR x 534 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR x 538 " --> pdb=" O LEU x 837 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN x 834 " --> pdb=" O ARG x 844 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'x' and resid 795 through 797 removed outlier: 3.744A pdb=" N TYR x 829 " --> pdb=" O ILE x 849 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1795 1.34 - 1.46: 767 1.46 - 1.57: 3137 1.57 - 1.69: 1 1.69 - 1.81: 57 Bond restraints: 5757 Sorted by residual: bond pdb=" CA ARG x 584 " pdb=" CB ARG x 584 " ideal model delta sigma weight residual 1.531 1.614 -0.083 3.12e-02 1.03e+03 7.09e+00 bond pdb=" C THR x 681 " pdb=" N PRO x 682 " ideal model delta sigma weight residual 1.337 1.352 -0.016 1.11e-02 8.12e+03 2.03e+00 bond pdb=" C ILE x 613 " pdb=" N PRO x 614 " ideal model delta sigma weight residual 1.336 1.352 -0.017 1.23e-02 6.61e+03 1.84e+00 bond pdb=" CB ARG x 584 " pdb=" CG ARG x 584 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.82e+00 bond pdb=" N ASP y 144 " pdb=" CA ASP y 144 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.77e-02 3.19e+03 1.53e+00 ... (remaining 5752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 7407 1.82 - 3.64: 305 3.64 - 5.46: 43 5.46 - 7.28: 15 7.28 - 9.10: 9 Bond angle restraints: 7779 Sorted by residual: angle pdb=" C HIS y 142 " pdb=" N PRO y 143 " pdb=" CA PRO y 143 " ideal model delta sigma weight residual 119.84 125.33 -5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" C VAL x 297 " pdb=" N LEU x 298 " pdb=" CA LEU x 298 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.82e+01 angle pdb=" CA ARG x 584 " pdb=" CB ARG x 584 " pdb=" CG ARG x 584 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" N LEU x 298 " pdb=" CA LEU x 298 " pdb=" C LEU x 298 " ideal model delta sigma weight residual 110.80 103.10 7.70 2.13e+00 2.20e-01 1.31e+01 angle pdb=" C LEU x 434 " pdb=" N PRO x 435 " pdb=" CD PRO x 435 " ideal model delta sigma weight residual 120.60 112.96 7.64 2.20e+00 2.07e-01 1.21e+01 ... (remaining 7774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.93: 3343 14.93 - 29.85: 137 29.85 - 44.77: 52 44.77 - 59.70: 6 59.70 - 74.62: 6 Dihedral angle restraints: 3544 sinusoidal: 1477 harmonic: 2067 Sorted by residual: dihedral pdb=" CA PHE x 605 " pdb=" C PHE x 605 " pdb=" N PRO x 606 " pdb=" CA PRO x 606 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA VAL x 297 " pdb=" C VAL x 297 " pdb=" N LEU x 298 " pdb=" CA LEU x 298 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU x 607 " pdb=" C LEU x 607 " pdb=" N MET x 608 " pdb=" CA MET x 608 " ideal model delta harmonic sigma weight residual -180.00 -158.66 -21.34 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 3541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 781 0.078 - 0.155: 110 0.155 - 0.233: 7 0.233 - 0.310: 2 0.310 - 0.388: 1 Chirality restraints: 901 Sorted by residual: chirality pdb=" CA ASP y 144 " pdb=" N ASP y 144 " pdb=" C ASP y 144 " pdb=" CB ASP y 144 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB ILE x 635 " pdb=" CA ILE x 635 " pdb=" CG1 ILE x 635 " pdb=" CG2 ILE x 635 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB THR x 585 " pdb=" CA THR x 585 " pdb=" OG1 THR x 585 " pdb=" CG2 THR x 585 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 898 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN x 757 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" CG ASN x 757 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN x 757 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN x 757 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS x 810 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO x 811 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO x 811 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO x 811 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR x 313 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO x 314 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO x 314 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO x 314 " -0.029 5.00e-02 4.00e+02 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1294 2.79 - 3.32: 4845 3.32 - 3.84: 8983 3.84 - 4.37: 10831 4.37 - 4.90: 18170 Nonbonded interactions: 44123 Sorted by model distance: nonbonded pdb=" OG1 THR x 636 " pdb=" O VAL y 89 " model vdw 2.260 3.040 nonbonded pdb=" O SER x 683 " pdb=" OG1 THR x 733 " model vdw 2.314 3.040 nonbonded pdb=" O SER x 717 " pdb=" OG SER x 720 " model vdw 2.335 3.040 nonbonded pdb=" O GLN x 427 " pdb=" OG1 THR x 431 " model vdw 2.338 3.040 nonbonded pdb=" NZ LYS x 689 " pdb=" OD1 ASP x 703 " model vdw 2.354 3.120 ... (remaining 44118 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.005 0.083 5757 Z= 0.327 Angle : 0.894 9.099 7779 Z= 0.464 Chirality : 0.055 0.388 901 Planarity : 0.007 0.053 986 Dihedral : 10.492 74.622 2204 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.00 % Favored : 96.72 % Rotamer: Outliers : 0.63 % Allowed : 3.93 % Favored : 95.44 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.78 % 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: -4.71 (0.24), residues: 701 helix: -4.37 (0.12), residues: 296 sheet: -0.85 (0.49), residues: 107 loop : -2.44 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP x 723 HIS 0.012 0.002 HIS x 810 PHE 0.013 0.002 PHE x 565 TYR 0.023 0.003 TYR x 321 ARG 0.005 0.001 ARG x 777 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: x 584 ARG cc_start: 0.6619 (pmt-80) cc_final: 0.5582 (ppt170) REVERT: x 854 TRP cc_start: 0.7522 (m-10) cc_final: 0.7105 (m-10) outliers start: 4 outliers final: 1 residues processed: 157 average time/residue: 0.2336 time to fit residues: 45.2180 Evaluate side-chains 91 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain y residue 144 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.0050 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 255 GLN x 258 GLN x 315 ASN x 408 HIS x 727 HIS x 796 GLN y 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.152466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123410 restraints weight = 6479.111| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.19 r_work: 0.3364 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5757 Z= 0.169 Angle : 0.561 5.148 7779 Z= 0.293 Chirality : 0.044 0.169 901 Planarity : 0.005 0.041 986 Dihedral : 5.209 49.665 765 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.52 % Allowed : 7.08 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -2.95 (0.28), residues: 701 helix: -2.46 (0.23), residues: 306 sheet: -0.46 (0.51), residues: 107 loop : -1.77 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP x 568 HIS 0.004 0.001 HIS x 810 PHE 0.009 0.001 PHE x 731 TYR 0.012 0.001 TYR x 832 ARG 0.006 0.000 ARG x 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 447 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7635 (mt-10) REVERT: x 575 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7943 (mm-30) REVERT: x 584 ARG cc_start: 0.6621 (pmt-80) cc_final: 0.5894 (pmt-80) REVERT: x 847 LEU cc_start: 0.8217 (tm) cc_final: 0.7997 (tp) outliers start: 16 outliers final: 6 residues processed: 104 average time/residue: 0.2314 time to fit residues: 29.9716 Evaluate side-chains 80 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 522 VAL Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 815 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 0.0010 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116964 restraints weight = 6660.833| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.15 r_work: 0.3279 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5757 Z= 0.277 Angle : 0.611 6.220 7779 Z= 0.311 Chirality : 0.047 0.247 901 Planarity : 0.005 0.041 986 Dihedral : 4.656 18.844 763 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.36 % Allowed : 9.43 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.95 (0.31), residues: 701 helix: -1.30 (0.28), residues: 307 sheet: -0.59 (0.51), residues: 105 loop : -1.38 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP x 568 HIS 0.003 0.001 HIS x 810 PHE 0.015 0.002 PHE x 719 TYR 0.023 0.002 TYR x 832 ARG 0.004 0.000 ARG x 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: x 279 ARG cc_start: 0.8555 (tpp80) cc_final: 0.7619 (mtm110) REVERT: x 347 GLU cc_start: 0.8419 (mp0) cc_final: 0.8149 (mm-30) REVERT: x 575 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8129 (mm-30) REVERT: x 584 ARG cc_start: 0.6746 (pmt-80) cc_final: 0.6022 (pmt-80) REVERT: x 847 LEU cc_start: 0.8426 (tm) cc_final: 0.8154 (tp) REVERT: x 854 TRP cc_start: 0.8079 (m-10) cc_final: 0.7296 (m-10) outliers start: 15 outliers final: 8 residues processed: 89 average time/residue: 0.2356 time to fit residues: 26.6321 Evaluate side-chains 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 522 VAL Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 619 SER Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 812 THR Chi-restraints excluded: chain x residue 815 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121273 restraints weight = 6715.433| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.14 r_work: 0.3329 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5757 Z= 0.162 Angle : 0.523 5.211 7779 Z= 0.266 Chirality : 0.044 0.234 901 Planarity : 0.004 0.039 986 Dihedral : 4.317 17.034 763 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.73 % Allowed : 11.64 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.31 (0.32), residues: 701 helix: -0.55 (0.29), residues: 306 sheet: -0.44 (0.52), residues: 105 loop : -1.24 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP x 568 HIS 0.004 0.001 HIS x 810 PHE 0.008 0.001 PHE x 779 TYR 0.013 0.001 TYR x 832 ARG 0.004 0.000 ARG x 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: x 347 GLU cc_start: 0.8344 (mp0) cc_final: 0.8065 (mm-30) REVERT: x 575 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8112 (mm-30) REVERT: x 584 ARG cc_start: 0.6559 (pmt-80) cc_final: 0.5567 (ppt170) REVERT: x 854 TRP cc_start: 0.8005 (m-10) cc_final: 0.7246 (m-10) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.2375 time to fit residues: 25.7678 Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 619 SER Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 815 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.0040 chunk 66 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 239 ASN x 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121686 restraints weight = 6596.575| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.16 r_work: 0.3348 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5757 Z= 0.153 Angle : 0.506 5.745 7779 Z= 0.258 Chirality : 0.043 0.223 901 Planarity : 0.004 0.037 986 Dihedral : 4.172 16.000 763 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.20 % Allowed : 12.74 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.77 (0.32), residues: 701 helix: 0.03 (0.30), residues: 306 sheet: -0.43 (0.49), residues: 115 loop : -1.02 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 568 HIS 0.003 0.001 HIS x 810 PHE 0.007 0.001 PHE x 779 TYR 0.014 0.001 TYR x 832 ARG 0.005 0.000 ARG x 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: x 575 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8183 (mm-30) REVERT: x 584 ARG cc_start: 0.6519 (pmt-80) cc_final: 0.5821 (pmt-80) REVERT: x 854 TRP cc_start: 0.7991 (m-10) cc_final: 0.7174 (m-10) REVERT: y 71 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5801 (mt) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.2029 time to fit residues: 22.1202 Evaluate side-chains 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 522 VAL Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 619 SER Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 812 THR Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 239 ASN ** 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 = 0.3813 r_free = 0.3813 target = 0.150817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121124 restraints weight = 6615.647| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.19 r_work: 0.3329 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5757 Z= 0.162 Angle : 0.511 5.110 7779 Z= 0.262 Chirality : 0.044 0.205 901 Planarity : 0.004 0.035 986 Dihedral : 4.133 15.977 763 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.52 % Allowed : 13.21 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.53 (0.33), residues: 701 helix: 0.32 (0.30), residues: 306 sheet: -0.32 (0.50), residues: 119 loop : -1.00 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 568 HIS 0.003 0.001 HIS x 810 PHE 0.009 0.001 PHE x 779 TYR 0.014 0.001 TYR x 832 ARG 0.006 0.000 ARG x 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: x 294 MET cc_start: 0.7292 (ttt) cc_final: 0.7002 (ttm) REVERT: x 372 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8283 (tp) REVERT: x 575 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8133 (mm-30) REVERT: x 584 ARG cc_start: 0.6512 (pmt-80) cc_final: 0.5722 (pmt-80) REVERT: x 854 TRP cc_start: 0.8008 (m-10) cc_final: 0.7183 (m-10) REVERT: y 71 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5776 (mt) outliers start: 16 outliers final: 7 residues processed: 82 average time/residue: 0.1884 time to fit residues: 20.3424 Evaluate side-chains 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 372 LEU Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 522 VAL Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 619 SER Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 812 THR Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 239 ASN x 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121392 restraints weight = 6644.968| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.18 r_work: 0.3335 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5757 Z= 0.177 Angle : 0.531 5.618 7779 Z= 0.268 Chirality : 0.044 0.188 901 Planarity : 0.004 0.037 986 Dihedral : 4.122 15.966 763 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.52 % Allowed : 13.36 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.32 (0.33), residues: 701 helix: 0.51 (0.31), residues: 306 sheet: -0.22 (0.50), residues: 119 loop : -0.92 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 810 PHE 0.010 0.001 PHE x 779 TYR 0.015 0.001 TYR x 832 ARG 0.006 0.000 ARG x 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 294 MET cc_start: 0.7300 (ttt) cc_final: 0.7043 (ttm) REVERT: x 301 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: x 372 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8309 (tp) REVERT: x 584 ARG cc_start: 0.6487 (pmt-80) cc_final: 0.5713 (pmt-80) REVERT: x 854 TRP cc_start: 0.7999 (m-10) cc_final: 0.7166 (m-10) REVERT: y 71 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5748 (mt) outliers start: 16 outliers final: 9 residues processed: 82 average time/residue: 0.2129 time to fit residues: 22.4521 Evaluate side-chains 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 372 LEU Chi-restraints excluded: chain x residue 443 THR Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 522 VAL Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 619 SER Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 812 THR Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 59 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 239 ASN x 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122748 restraints weight = 6596.482| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.17 r_work: 0.3349 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5757 Z= 0.152 Angle : 0.506 5.199 7779 Z= 0.256 Chirality : 0.043 0.163 901 Planarity : 0.004 0.039 986 Dihedral : 4.054 15.684 763 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.20 % Allowed : 14.47 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.11 (0.33), residues: 701 helix: 0.75 (0.31), residues: 306 sheet: -0.14 (0.50), residues: 119 loop : -0.88 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 568 HIS 0.005 0.001 HIS x 810 PHE 0.008 0.001 PHE x 779 TYR 0.013 0.001 TYR x 832 ARG 0.007 0.000 ARG x 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: x 294 MET cc_start: 0.7325 (ttt) cc_final: 0.7069 (ttm) REVERT: x 372 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8317 (tp) REVERT: x 584 ARG cc_start: 0.6470 (pmt-80) cc_final: 0.5926 (pmt-80) REVERT: x 854 TRP cc_start: 0.7986 (m-10) cc_final: 0.7150 (m-10) REVERT: y 71 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.5759 (mt) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.1749 time to fit residues: 19.2682 Evaluate side-chains 79 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 372 LEU Chi-restraints excluded: chain x residue 443 THR Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 522 VAL Chi-restraints excluded: chain x residue 576 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 619 SER Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 812 THR Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 572 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123074 restraints weight = 6606.450| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.19 r_work: 0.3348 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5757 Z= 0.162 Angle : 0.526 5.514 7779 Z= 0.269 Chirality : 0.044 0.162 901 Planarity : 0.004 0.038 986 Dihedral : 4.024 15.617 763 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.36 % Allowed : 14.15 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.07 (0.33), residues: 701 helix: 0.93 (0.31), residues: 306 sheet: -0.02 (0.51), residues: 119 loop : -0.85 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 568 HIS 0.005 0.001 HIS x 810 PHE 0.008 0.001 PHE x 779 TYR 0.012 0.001 TYR x 832 ARG 0.007 0.000 ARG x 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 294 MET cc_start: 0.7291 (ttt) cc_final: 0.7069 (ttm) REVERT: x 372 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8284 (tp) REVERT: x 584 ARG cc_start: 0.6543 (pmt-80) cc_final: 0.5994 (pmt-80) REVERT: x 854 TRP cc_start: 0.7995 (m-10) cc_final: 0.7190 (m-10) REVERT: y 71 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.5733 (mt) outliers start: 15 outliers final: 10 residues processed: 78 average time/residue: 0.1891 time to fit residues: 19.4443 Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 372 LEU Chi-restraints excluded: chain x residue 443 THR Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 522 VAL Chi-restraints excluded: chain x residue 576 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 619 SER Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 812 THR Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.0170 chunk 66 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 69 optimal weight: 0.0170 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 502 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123718 restraints weight = 6635.094| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.23 r_work: 0.3360 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5757 Z= 0.146 Angle : 0.507 5.391 7779 Z= 0.259 Chirality : 0.043 0.157 901 Planarity : 0.004 0.037 986 Dihedral : 3.950 15.269 763 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.89 % Allowed : 14.94 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.32 (0.33), residues: 701 helix: 1.25 (0.31), residues: 302 sheet: 0.01 (0.51), residues: 119 loop : -0.78 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 568 HIS 0.005 0.001 HIS x 810 PHE 0.007 0.001 PHE x 779 TYR 0.011 0.001 TYR x 832 ARG 0.008 0.000 ARG x 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 294 MET cc_start: 0.7357 (ttt) cc_final: 0.7130 (ttm) REVERT: x 854 TRP cc_start: 0.7974 (m-10) cc_final: 0.7192 (m-10) REVERT: y 71 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5696 (mt) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.2024 time to fit residues: 19.4792 Evaluate side-chains 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 225 VAL Chi-restraints excluded: chain x residue 443 THR Chi-restraints excluded: chain x residue 522 VAL Chi-restraints excluded: chain x residue 576 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 619 SER Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 812 THR Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 502 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123306 restraints weight = 6615.393| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.14 r_work: 0.3362 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5757 Z= 0.157 Angle : 0.515 6.940 7779 Z= 0.262 Chirality : 0.043 0.167 901 Planarity : 0.004 0.037 986 Dihedral : 3.926 15.353 763 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.20 % Allowed : 14.94 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.33), residues: 701 helix: 1.43 (0.31), residues: 301 sheet: 0.11 (0.51), residues: 119 loop : -0.81 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 568 HIS 0.005 0.001 HIS x 810 PHE 0.008 0.001 PHE x 779 TYR 0.012 0.001 TYR x 832 ARG 0.008 0.000 ARG x 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4126.83 seconds wall clock time: 73 minutes 48.54 seconds (4428.54 seconds total)