Starting phenix.real_space_refine on Mon Mar 11 17:09:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9f_9014/03_2024/6e9f_9014.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9f_9014/03_2024/6e9f_9014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9f_9014/03_2024/6e9f_9014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9f_9014/03_2024/6e9f_9014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9f_9014/03_2024/6e9f_9014.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9f_9014/03_2024/6e9f_9014.pdb" } resolution = 3.3 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 79 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 5245 2.51 5 N 1491 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 630": "NH1" <-> "NH2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8745 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 7065 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 13, 'TRANS': 850} Chain breaks: 5 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1110 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 21} Link IDs: {'rna2p': 7, 'rna3p': 44} Chain: "C" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 569 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 15} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.59 Number of scatterers: 8745 At special positions: 0 Unit cell: (106.65, 80.58, 97.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 79 15.00 Mg 1 11.99 O 1899 8.00 N 1491 7.00 C 5245 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: 3.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 57.5% alpha, 3.0% beta 23 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 159 through 168 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.053A pdb=" N ASP A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.525A pdb=" N ASP A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.556A pdb=" N TYR A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.902A pdb=" N LEU A 313 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 315 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.695A pdb=" N LYS A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.583A pdb=" N VAL A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.581A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 381 through 390 removed outlier: 4.531A pdb=" N GLU A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.729A pdb=" N ASP A 401 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 402 " --> pdb=" O GLU A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 403 through 422 removed outlier: 4.135A pdb=" N GLN A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.634A pdb=" N ALA A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 445 Processing helix chain 'A' and resid 446 through 467 removed outlier: 4.517A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.852A pdb=" N PHE A 493 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 3.513A pdb=" N THR A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.941A pdb=" N ASN A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.533A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 558 through 571 removed outlier: 3.636A pdb=" N ALA A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 595 removed outlier: 3.693A pdb=" N LEU A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 604 Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 628 through 640 removed outlier: 3.686A pdb=" N ILE A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 647 removed outlier: 3.544A pdb=" N LYS A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.895A pdb=" N LYS A 654 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 655 " --> pdb=" O PRO A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 655' Processing helix chain 'A' and resid 661 through 669 Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.565A pdb=" N ARG A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 706 removed outlier: 3.602A pdb=" N ARG A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 removed outlier: 4.406A pdb=" N LYS A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 758 removed outlier: 3.971A pdb=" N TYR A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.837A pdb=" N TYR A 762 " --> pdb=" O VAL A 758 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU A 770 " --> pdb=" O PHE A 766 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 797 Processing helix chain 'A' and resid 826 through 838 removed outlier: 3.790A pdb=" N ILE A 833 " --> pdb=" O TRP A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 853 removed outlier: 3.929A pdb=" N VAL A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 removed outlier: 4.169A pdb=" N HIS A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 removed outlier: 4.097A pdb=" N PHE A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 903 " --> pdb=" O THR A 899 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 904 " --> pdb=" O GLY A 900 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 909 " --> pdb=" O LYS A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.557A pdb=" N TYR A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 removed outlier: 3.600A pdb=" N PHE A 924 " --> pdb=" O CYS A 921 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82 removed outlier: 3.521A pdb=" N VAL A 89 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95 removed outlier: 3.628A pdb=" N VAL A 95 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 114 removed outlier: 6.807A pdb=" N SER A 120 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL A 114 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265 252 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2309 1.33 - 1.45: 2182 1.45 - 1.57: 4364 1.57 - 1.69: 156 1.69 - 1.81: 47 Bond restraints: 9058 Sorted by residual: bond pdb=" N LYS A 160 " pdb=" CA LYS A 160 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.19e+00 bond pdb=" N LEU A 159 " pdb=" CA LEU A 159 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N LYS A 165 " pdb=" CA LYS A 165 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.23e+00 bond pdb=" N THR A 922 " pdb=" CA THR A 922 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.04e-02 9.25e+03 7.19e+00 bond pdb=" CB PRO A 923 " pdb=" CG PRO A 923 " ideal model delta sigma weight residual 1.492 1.368 0.124 5.00e-02 4.00e+02 6.19e+00 ... (remaining 9053 not shown) Histogram of bond angle deviations from ideal: 96.78 - 105.22: 421 105.22 - 113.66: 5227 113.66 - 122.10: 5382 122.10 - 130.53: 1491 130.53 - 138.97: 50 Bond angle restraints: 12571 Sorted by residual: angle pdb=" N CYS A 921 " pdb=" CA CYS A 921 " pdb=" C CYS A 921 " ideal model delta sigma weight residual 113.17 105.61 7.56 1.26e+00 6.30e-01 3.60e+01 angle pdb=" C THR A 922 " pdb=" N PRO A 923 " pdb=" CA PRO A 923 " ideal model delta sigma weight residual 119.84 112.63 7.21 1.25e+00 6.40e-01 3.33e+01 angle pdb=" N LEU A 111 " pdb=" CA LEU A 111 " pdb=" C LEU A 111 " ideal model delta sigma weight residual 109.24 118.32 -9.08 1.63e+00 3.76e-01 3.11e+01 angle pdb=" N VAL A 523 " pdb=" CA VAL A 523 " pdb=" C VAL A 523 " ideal model delta sigma weight residual 111.91 107.19 4.72 8.90e-01 1.26e+00 2.81e+01 angle pdb=" N ILE A 882 " pdb=" CA ILE A 882 " pdb=" C ILE A 882 " ideal model delta sigma weight residual 113.53 109.01 4.52 9.80e-01 1.04e+00 2.12e+01 ... (remaining 12566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.84: 5074 19.84 - 39.68: 334 39.68 - 59.51: 106 59.51 - 79.35: 54 79.35 - 99.19: 6 Dihedral angle restraints: 5574 sinusoidal: 3005 harmonic: 2569 Sorted by residual: dihedral pdb=" CA ILE A 494 " pdb=" C ILE A 494 " pdb=" N SER A 495 " pdb=" CA SER A 495 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ILE A 94 " pdb=" C ILE A 94 " pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA GLU A 518 " pdb=" C GLU A 518 " pdb=" N ILE A 519 " pdb=" CA ILE A 519 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1047 0.068 - 0.135: 328 0.135 - 0.203: 71 0.203 - 0.271: 9 0.271 - 0.338: 4 Chirality restraints: 1459 Sorted by residual: chirality pdb=" CB VAL A 523 " pdb=" CA VAL A 523 " pdb=" CG1 VAL A 523 " pdb=" CG2 VAL A 523 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA LYS A 273 " pdb=" N LYS A 273 " pdb=" C LYS A 273 " pdb=" CB LYS A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE A 484 " pdb=" CA ILE A 484 " pdb=" CG1 ILE A 484 " pdb=" CG2 ILE A 484 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1456 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 330 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO A 331 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 38 " 0.032 2.00e-02 2.50e+03 1.70e-02 7.91e+00 pdb=" N9 A B 38 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B 38 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A B 38 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A B 38 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 38 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 38 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A B 38 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A B 38 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 38 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 38 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 916 " 0.023 2.00e-02 2.50e+03 2.06e-02 7.43e+00 pdb=" CG PHE A 916 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 916 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 916 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 916 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 916 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 916 " 0.002 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 72 2.48 - 3.08: 5891 3.08 - 3.69: 14370 3.69 - 4.29: 20924 4.29 - 4.90: 32380 Nonbonded interactions: 73637 Sorted by model distance: nonbonded pdb=" O4 U C 4 " pdb=" N3 U C 5 " model vdw 1.872 2.520 nonbonded pdb=" O2' A B 32 " pdb=" O5' C B 33 " model vdw 2.091 2.440 nonbonded pdb=" OP1 U B 23 " pdb="MG MG B 101 " model vdw 2.102 2.170 nonbonded pdb=" N1 G B 22 " pdb=" N6 A B 28 " model vdw 2.169 3.200 nonbonded pdb=" C4 U C 4 " pdb=" N3 U C 5 " model vdw 2.178 3.340 ... (remaining 73632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.810 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: 0.000 Extract box with map and model: 4.110 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.330 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.011 0.124 9058 Z= 0.715 Angle : 1.131 13.972 12571 Z= 0.620 Chirality : 0.069 0.338 1459 Planarity : 0.006 0.077 1316 Dihedral : 16.250 99.187 3910 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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: -5.59 (0.20), residues: 852 helix: -4.18 (0.13), residues: 473 sheet: -4.08 (0.83), residues: 25 loop : -2.73 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 829 HIS 0.011 0.002 HIS A 885 PHE 0.048 0.004 PHE A 916 TYR 0.028 0.004 TYR A 912 ARG 0.014 0.002 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.902 Fit side-chains REVERT: A 223 ASP cc_start: 0.8179 (t70) cc_final: 0.7925 (t0) REVERT: A 241 LYS cc_start: 0.7553 (tttp) cc_final: 0.7239 (tptp) REVERT: A 338 ARG cc_start: 0.7152 (mtm110) cc_final: 0.6853 (mmp80) REVERT: A 375 TYR cc_start: 0.7400 (m-10) cc_final: 0.7167 (m-10) REVERT: A 479 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7356 (ttpp) REVERT: A 541 ASP cc_start: 0.7579 (t0) cc_final: 0.7297 (t0) REVERT: A 768 CYS cc_start: 0.7385 (m) cc_final: 0.6968 (m) REVERT: A 888 ASN cc_start: 0.7821 (t0) cc_final: 0.7558 (m-40) REVERT: A 896 GLU cc_start: 0.6622 (pm20) cc_final: 0.6219 (tp30) REVERT: A 926 TYR cc_start: 0.7934 (p90) cc_final: 0.7694 (p90) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2897 time to fit residues: 84.1601 Evaluate side-chains 118 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 348 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 885 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9058 Z= 0.191 Angle : 0.631 7.920 12571 Z= 0.332 Chirality : 0.041 0.169 1459 Planarity : 0.004 0.048 1316 Dihedral : 17.852 89.318 2131 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.61 % Allowed : 12.24 % Favored : 84.15 % 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: -4.20 (0.24), residues: 852 helix: -2.89 (0.18), residues: 501 sheet: -3.85 (0.86), residues: 25 loop : -2.22 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 309 HIS 0.005 0.001 HIS A 879 PHE 0.017 0.002 PHE A 167 TYR 0.012 0.002 TYR A 416 ARG 0.008 0.001 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8274 (t70) cc_final: 0.8029 (t0) REVERT: A 240 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6315 (mt-10) REVERT: A 241 LYS cc_start: 0.7661 (tttp) cc_final: 0.7243 (tptp) REVERT: A 261 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6781 (t0) REVERT: A 338 ARG cc_start: 0.6798 (mtm110) cc_final: 0.6418 (mmp80) REVERT: A 479 LYS cc_start: 0.8326 (mtpp) cc_final: 0.7727 (ttpp) REVERT: A 682 GLU cc_start: 0.7924 (tp30) cc_final: 0.7659 (tp30) REVERT: A 832 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7355 (mt) REVERT: A 888 ASN cc_start: 0.7778 (t0) cc_final: 0.7380 (m-40) REVERT: A 896 GLU cc_start: 0.6576 (pm20) cc_final: 0.6243 (tp30) outliers start: 28 outliers final: 20 residues processed: 173 average time/residue: 0.2222 time to fit residues: 53.1785 Evaluate side-chains 145 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 103 ASN A 346 ASN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9058 Z= 0.195 Angle : 0.580 7.391 12571 Z= 0.304 Chirality : 0.039 0.143 1459 Planarity : 0.004 0.043 1316 Dihedral : 17.589 90.269 2131 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.64 % Allowed : 14.56 % Favored : 80.80 % 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: -3.15 (0.27), residues: 852 helix: -2.02 (0.21), residues: 498 sheet: -3.52 (0.88), residues: 25 loop : -1.79 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 309 HIS 0.005 0.001 HIS A 879 PHE 0.018 0.002 PHE A 848 TYR 0.017 0.002 TYR A 926 ARG 0.006 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7559 (pt0) cc_final: 0.7357 (pt0) REVERT: A 241 LYS cc_start: 0.7767 (tttp) cc_final: 0.7219 (tptp) REVERT: A 454 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 479 LYS cc_start: 0.8556 (mtpp) cc_final: 0.7998 (ttpt) REVERT: A 491 LYS cc_start: 0.8294 (pttt) cc_final: 0.7941 (pttm) REVERT: A 514 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8526 (pp) REVERT: A 645 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: A 682 GLU cc_start: 0.7895 (tp30) cc_final: 0.7551 (tp30) REVERT: A 832 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7376 (mt) REVERT: A 888 ASN cc_start: 0.7797 (t0) cc_final: 0.7391 (m-40) REVERT: A 896 GLU cc_start: 0.6446 (pm20) cc_final: 0.6198 (tp30) outliers start: 36 outliers final: 21 residues processed: 155 average time/residue: 0.2138 time to fit residues: 45.9558 Evaluate side-chains 145 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 936 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9058 Z= 0.218 Angle : 0.589 9.815 12571 Z= 0.302 Chirality : 0.040 0.145 1459 Planarity : 0.004 0.041 1316 Dihedral : 17.422 91.271 2131 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.90 % Allowed : 15.85 % Favored : 79.25 % 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: -2.56 (0.27), residues: 852 helix: -1.55 (0.22), residues: 496 sheet: -3.45 (0.91), residues: 24 loop : -1.53 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 309 HIS 0.005 0.001 HIS A 879 PHE 0.016 0.002 PHE A 848 TYR 0.029 0.002 TYR A 926 ARG 0.004 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8050 (tpp) cc_final: 0.7785 (tpp) REVERT: A 241 LYS cc_start: 0.7916 (tttp) cc_final: 0.7347 (tptp) REVERT: A 307 GLU cc_start: 0.6032 (tm-30) cc_final: 0.5664 (tm-30) REVERT: A 479 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8095 (tmmt) REVERT: A 514 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8507 (pp) REVERT: A 645 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7641 (m-10) REVERT: A 682 GLU cc_start: 0.7922 (tp30) cc_final: 0.7588 (tp30) REVERT: A 832 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7058 (mt) REVERT: A 888 ASN cc_start: 0.7751 (t0) cc_final: 0.7314 (m110) outliers start: 38 outliers final: 23 residues processed: 149 average time/residue: 0.2181 time to fit residues: 44.4489 Evaluate side-chains 141 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9058 Z= 0.260 Angle : 0.597 7.696 12571 Z= 0.310 Chirality : 0.041 0.153 1459 Planarity : 0.004 0.042 1316 Dihedral : 17.385 92.673 2131 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.15 % Allowed : 16.75 % Favored : 78.09 % 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: -2.23 (0.28), residues: 852 helix: -1.26 (0.23), residues: 500 sheet: -3.46 (0.89), residues: 24 loop : -1.44 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 297 HIS 0.005 0.001 HIS A 879 PHE 0.017 0.002 PHE A 848 TYR 0.029 0.002 TYR A 926 ARG 0.004 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.7930 (tpp) cc_final: 0.7720 (tpp) REVERT: A 241 LYS cc_start: 0.8056 (tttp) cc_final: 0.7389 (tptp) REVERT: A 307 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5649 (tm-30) REVERT: A 479 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8143 (tmmt) REVERT: A 645 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: A 682 GLU cc_start: 0.7977 (tp30) cc_final: 0.7676 (tp30) REVERT: A 832 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7237 (mt) REVERT: A 868 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 888 ASN cc_start: 0.7737 (t0) cc_final: 0.7288 (m110) REVERT: A 897 ARG cc_start: 0.7425 (ttp80) cc_final: 0.7109 (ttp80) outliers start: 40 outliers final: 24 residues processed: 153 average time/residue: 0.2241 time to fit residues: 46.7108 Evaluate side-chains 142 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 943 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 0.0470 chunk 47 optimal weight: 5.9990 overall best weight: 2.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9058 Z= 0.288 Angle : 0.622 7.430 12571 Z= 0.324 Chirality : 0.042 0.157 1459 Planarity : 0.004 0.043 1316 Dihedral : 17.380 94.560 2131 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.90 % Allowed : 18.04 % Favored : 77.06 % 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: -2.09 (0.28), residues: 852 helix: -1.15 (0.23), residues: 501 sheet: -3.07 (0.87), residues: 25 loop : -1.38 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 297 HIS 0.006 0.001 HIS A 879 PHE 0.018 0.002 PHE A 916 TYR 0.030 0.002 TYR A 926 ARG 0.004 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 307 GLU cc_start: 0.6081 (tm-30) cc_final: 0.5845 (tm-30) REVERT: A 384 LYS cc_start: 0.7717 (tttt) cc_final: 0.7155 (ttmt) REVERT: A 479 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8169 (tmmt) REVERT: A 579 ASP cc_start: 0.7100 (p0) cc_final: 0.6735 (p0) REVERT: A 645 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7534 (m-10) REVERT: A 671 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: A 682 GLU cc_start: 0.8016 (tp30) cc_final: 0.7811 (tp30) REVERT: A 832 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7303 (mt) REVERT: A 868 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 888 ASN cc_start: 0.7820 (t0) cc_final: 0.7282 (m110) REVERT: A 897 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7289 (tmm-80) outliers start: 38 outliers final: 26 residues processed: 147 average time/residue: 0.2275 time to fit residues: 45.1847 Evaluate side-chains 140 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9058 Z= 0.262 Angle : 0.612 9.021 12571 Z= 0.315 Chirality : 0.041 0.169 1459 Planarity : 0.004 0.044 1316 Dihedral : 17.349 95.192 2131 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.64 % Allowed : 20.10 % Favored : 75.26 % 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: -1.92 (0.28), residues: 852 helix: -0.99 (0.24), residues: 489 sheet: -3.01 (0.86), residues: 25 loop : -1.36 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 297 HIS 0.006 0.001 HIS A 879 PHE 0.014 0.002 PHE A 916 TYR 0.030 0.002 TYR A 926 ARG 0.004 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.7539 (tpt) cc_final: 0.7168 (tpt) REVERT: A 205 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8261 (mmm) REVERT: A 307 GLU cc_start: 0.6011 (tm-30) cc_final: 0.5700 (tm-30) REVERT: A 479 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8165 (tmmt) REVERT: A 491 LYS cc_start: 0.8514 (pttt) cc_final: 0.8311 (pttm) REVERT: A 645 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7533 (m-10) REVERT: A 671 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7579 (pp20) REVERT: A 682 GLU cc_start: 0.8022 (tp30) cc_final: 0.7814 (tp30) REVERT: A 832 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7254 (mt) REVERT: A 868 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8399 (mt) outliers start: 36 outliers final: 23 residues processed: 145 average time/residue: 0.2372 time to fit residues: 46.9182 Evaluate side-chains 140 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.0170 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 0.0670 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 85 optimal weight: 6.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 9058 Z= 0.154 Angle : 0.536 7.383 12571 Z= 0.274 Chirality : 0.037 0.132 1459 Planarity : 0.003 0.043 1316 Dihedral : 17.201 93.694 2131 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.64 % Allowed : 20.23 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.29), residues: 852 helix: -0.78 (0.24), residues: 503 sheet: -3.09 (0.86), residues: 24 loop : -1.03 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 455 HIS 0.005 0.001 HIS A 879 PHE 0.017 0.001 PHE A 848 TYR 0.029 0.001 TYR A 926 ARG 0.004 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.7407 (tpt) cc_final: 0.7110 (tpt) REVERT: A 205 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8180 (mmm) REVERT: A 275 LYS cc_start: 0.7035 (tptt) cc_final: 0.6444 (ttpt) REVERT: A 449 LYS cc_start: 0.8034 (tptp) cc_final: 0.7799 (tppt) REVERT: A 479 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8239 (tmmt) REVERT: A 491 LYS cc_start: 0.8393 (pttt) cc_final: 0.8136 (pttm) REVERT: A 553 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7507 (t80) REVERT: A 613 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 832 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7135 (mt) outliers start: 36 outliers final: 21 residues processed: 155 average time/residue: 0.2119 time to fit residues: 44.8397 Evaluate side-chains 154 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0970 chunk 83 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 88 optimal weight: 7.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9058 Z= 0.173 Angle : 0.550 7.307 12571 Z= 0.282 Chirality : 0.038 0.136 1459 Planarity : 0.003 0.051 1316 Dihedral : 17.124 93.784 2131 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.74 % Allowed : 21.65 % Favored : 74.61 % 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: -1.34 (0.29), residues: 852 helix: -0.59 (0.24), residues: 496 sheet: -2.86 (0.87), residues: 24 loop : -0.98 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 PHE 0.016 0.001 PHE A 848 TYR 0.036 0.001 TYR A 926 ARG 0.010 0.000 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7309 (tpt) cc_final: 0.6979 (tpt) REVERT: A 205 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8225 (mmm) REVERT: A 275 LYS cc_start: 0.7000 (tptt) cc_final: 0.6474 (ttpt) REVERT: A 449 LYS cc_start: 0.8057 (tptp) cc_final: 0.7828 (tppt) REVERT: A 476 LYS cc_start: 0.7859 (ptmm) cc_final: 0.7659 (ptmm) REVERT: A 479 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8225 (tmmt) REVERT: A 531 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7913 (t0) REVERT: A 553 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7802 (t80) REVERT: A 613 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8163 (mm) REVERT: A 832 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7195 (mt) outliers start: 29 outliers final: 17 residues processed: 144 average time/residue: 0.2351 time to fit residues: 45.3377 Evaluate side-chains 142 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9058 Z= 0.218 Angle : 0.580 7.520 12571 Z= 0.298 Chirality : 0.040 0.146 1459 Planarity : 0.003 0.044 1316 Dihedral : 17.126 94.317 2131 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.48 % Allowed : 22.16 % Favored : 74.36 % 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: -1.30 (0.29), residues: 852 helix: -0.54 (0.24), residues: 498 sheet: -2.67 (0.89), residues: 24 loop : -1.01 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 297 HIS 0.005 0.001 HIS A 879 PHE 0.012 0.002 PHE A 924 TYR 0.039 0.002 TYR A 926 ARG 0.008 0.000 ARG A 897 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.7244 (tpt) cc_final: 0.6882 (tpt) REVERT: A 205 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: A 275 LYS cc_start: 0.6973 (tptt) cc_final: 0.6506 (ttpt) REVERT: A 449 LYS cc_start: 0.8114 (tptp) cc_final: 0.7898 (tppt) REVERT: A 476 LYS cc_start: 0.7840 (ptmm) cc_final: 0.7628 (ptmm) REVERT: A 479 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8233 (tmmt) REVERT: A 613 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 832 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7258 (mt) REVERT: A 868 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8293 (mt) outliers start: 27 outliers final: 19 residues processed: 130 average time/residue: 0.2230 time to fit residues: 39.5473 Evaluate side-chains 135 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118320 restraints weight = 13191.605| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.70 r_work: 0.3253 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9058 Z= 0.204 Angle : 0.572 7.357 12571 Z= 0.292 Chirality : 0.039 0.142 1459 Planarity : 0.003 0.044 1316 Dihedral : 17.117 94.564 2131 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.87 % Allowed : 21.78 % Favored : 74.36 % 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: -1.19 (0.29), residues: 852 helix: -0.46 (0.24), residues: 493 sheet: -2.50 (0.91), residues: 24 loop : -0.96 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.005 0.001 HIS A 879 PHE 0.013 0.001 PHE A 308 TYR 0.035 0.002 TYR A 926 ARG 0.008 0.000 ARG A 897 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.16 seconds wall clock time: 37 minutes 9.09 seconds (2229.09 seconds total)