Starting phenix.real_space_refine on Thu Nov 14 18:57:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcn_29936/11_2024/8gcn_29936.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcn_29936/11_2024/8gcn_29936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcn_29936/11_2024/8gcn_29936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcn_29936/11_2024/8gcn_29936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcn_29936/11_2024/8gcn_29936.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcn_29936/11_2024/8gcn_29936.cif" } resolution = 3.95 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= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4507 2.51 5 N 1224 2.21 5 O 1393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7173 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6805 Classifications: {'peptide': 876} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 838} Chain: "B" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 368 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Time building chain proxies: 4.08, per 1000 atoms: 0.57 Number of scatterers: 7173 At special positions: 0 Unit cell: (81.096, 91.56, 112.488, 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 49 16.00 O 1393 8.00 N 1224 7.00 C 4507 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: 1.82 Conformation dependent library (CDL) restraints added in 974.8 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 32 Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.524A pdb=" N ASN A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.662A pdb=" N ALA A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.646A pdb=" N LEU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 124 removed outlier: 4.250A pdb=" N GLN A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 169 through 181 removed outlier: 4.007A pdb=" N ILE A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.788A pdb=" N LYS A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.894A pdb=" N ASP A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 230 through 248 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 272 through 304 Processing helix chain 'A' and resid 313 through 330 removed outlier: 5.536A pdb=" N GLN A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 343 through 360 Processing helix chain 'A' and resid 363 through 375 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.690A pdb=" N ARG A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 418 removed outlier: 3.582A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Proline residue: A 404 - end of helix Proline residue: A 411 - end of helix removed outlier: 3.987A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.068A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 removed outlier: 4.210A pdb=" N ALA A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 463 through 486 removed outlier: 4.676A pdb=" N ASN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 515 removed outlier: 3.900A pdb=" N GLN A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 4.483A pdb=" N HIS A 520 " --> pdb=" O PRO A 517 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASN A 522 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 523 " --> pdb=" O HIS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 538 removed outlier: 3.871A pdb=" N TYR A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 543 through 562 removed outlier: 3.744A pdb=" N MET A 555 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 removed outlier: 3.865A pdb=" N GLN A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 618 removed outlier: 3.972A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 618 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.129A pdb=" N GLN A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 649 removed outlier: 4.753A pdb=" N LEU A 644 " --> pdb=" O GLY A 641 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS A 645 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU A 648 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.984A pdb=" N CYS A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 679 " --> pdb=" O GLY A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 702 removed outlier: 4.063A pdb=" N ASP A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 725 removed outlier: 3.566A pdb=" N LEU A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 722 " --> pdb=" O GLY A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 745 removed outlier: 4.371A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 735 " --> pdb=" O TYR A 731 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 741 " --> pdb=" O ASN A 737 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 742 " --> pdb=" O THR A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 778 Processing helix chain 'A' and resid 784 through 792 removed outlier: 3.937A pdb=" N LEU A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Proline residue: A 792 - end of helix Processing helix chain 'A' and resid 793 through 807 Processing helix chain 'A' and resid 811 through 829 removed outlier: 3.546A pdb=" N GLY A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 821 " --> pdb=" O CYS A 817 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 839 removed outlier: 4.021A pdb=" N LYS A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 836 " --> pdb=" O ASP A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 853 removed outlier: 4.046A pdb=" N GLU A 845 " --> pdb=" O PRO A 841 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 849 " --> pdb=" O GLU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 874 removed outlier: 3.650A pdb=" N GLU A 868 " --> pdb=" O TRP A 864 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 23 through 52 497 hydrogen bonds defined for protein. 1443 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: 2.26 Time building geometry restraints manager: 2.09 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: 1858 1.33 - 1.45: 1169 1.45 - 1.57: 4183 1.57 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7285 Sorted by residual: bond pdb=" N GLU A 493 " pdb=" CA GLU A 493 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.04e-02 9.25e+03 7.99e+00 bond pdb=" N GLU A 492 " pdb=" CA GLU A 492 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.15e+00 bond pdb=" N GLN A 491 " pdb=" CA GLN A 491 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 5.97e+00 bond pdb=" C PRO A 494 " pdb=" O PRO A 494 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.10e-02 8.26e+03 3.58e+00 bond pdb=" CA GLN A 491 " pdb=" C GLN A 491 " ideal model delta sigma weight residual 1.519 1.536 -0.016 1.01e-02 9.80e+03 2.60e+00 ... (remaining 7280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 9757 2.91 - 5.82: 86 5.82 - 8.74: 22 8.74 - 11.65: 8 11.65 - 14.56: 2 Bond angle restraints: 9875 Sorted by residual: angle pdb=" CA LEU A 198 " pdb=" CB LEU A 198 " pdb=" CG LEU A 198 " ideal model delta sigma weight residual 116.30 130.86 -14.56 3.50e+00 8.16e-02 1.73e+01 angle pdb=" CA LEU A 416 " pdb=" CB LEU A 416 " pdb=" CG LEU A 416 " ideal model delta sigma weight residual 116.30 130.51 -14.21 3.50e+00 8.16e-02 1.65e+01 angle pdb=" CB LYS B 18 " pdb=" CG LYS B 18 " pdb=" CD LYS B 18 " ideal model delta sigma weight residual 111.30 120.14 -8.84 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB MET A 555 " pdb=" CG MET A 555 " pdb=" SD MET A 555 " ideal model delta sigma weight residual 112.70 123.54 -10.84 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CB MET B 47 " pdb=" CG MET B 47 " pdb=" SD MET B 47 " ideal model delta sigma weight residual 112.70 123.40 -10.70 3.00e+00 1.11e-01 1.27e+01 ... (remaining 9870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 3786 18.01 - 36.01: 533 36.01 - 54.02: 139 54.02 - 72.03: 31 72.03 - 90.03: 21 Dihedral angle restraints: 4510 sinusoidal: 1810 harmonic: 2700 Sorted by residual: dihedral pdb=" CA LEU A 562 " pdb=" C LEU A 562 " pdb=" N GLN A 563 " pdb=" CA GLN A 563 " ideal model delta harmonic sigma weight residual 180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN A 563 " pdb=" C GLN A 563 " pdb=" N MET A 564 " pdb=" CA MET A 564 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ALA A 259 " pdb=" C ALA A 259 " pdb=" N LEU A 260 " pdb=" CA LEU A 260 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1000 0.059 - 0.118: 143 0.118 - 0.177: 4 0.177 - 0.236: 0 0.236 - 0.295: 1 Chirality restraints: 1148 Sorted by residual: chirality pdb=" CG LEU A 202 " pdb=" CB LEU A 202 " pdb=" CD1 LEU A 202 " pdb=" CD2 LEU A 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB THR A 863 " pdb=" CA THR A 863 " pdb=" OG1 THR A 863 " pdb=" CG2 THR A 863 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA GLU A 493 " pdb=" N GLU A 493 " pdb=" C GLU A 493 " pdb=" CB GLU A 493 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1145 not shown) Planarity restraints: 1291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 396 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 397 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 397 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 397 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 490 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ASP A 490 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP A 490 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 491 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 479 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" CD GLU A 479 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 479 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 479 " -0.013 2.00e-02 2.50e+03 ... (remaining 1288 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 169 2.67 - 3.23: 8007 3.23 - 3.79: 12435 3.79 - 4.34: 15526 4.34 - 4.90: 23268 Nonbonded interactions: 59405 Sorted by model distance: nonbonded pdb=" O VAL A 547 " pdb=" OG1 THR A 551 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR A 827 " pdb=" OE2 GLU A 868 " model vdw 2.164 3.040 nonbonded pdb=" OD1 ASP A 690 " pdb=" OH TYR A 731 " model vdw 2.175 3.040 nonbonded pdb=" O LEU A 847 " pdb=" NH1 ARG A 851 " model vdw 2.190 3.120 nonbonded pdb=" OE2 GLU A 398 " pdb=" OG SER A 400 " model vdw 2.204 3.040 ... (remaining 59400 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.160 Find NCS groups from input model: 0.080 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7285 Z= 0.213 Angle : 0.777 14.562 9875 Z= 0.369 Chirality : 0.041 0.295 1148 Planarity : 0.004 0.065 1291 Dihedral : 18.905 90.034 2750 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.13 % Allowed : 33.42 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.29), residues: 915 helix: 0.66 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.49 (0.46), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 80 HIS 0.002 0.001 HIS A 706 PHE 0.014 0.001 PHE A 577 TYR 0.031 0.001 TYR A 482 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.9580 (mmm) cc_final: 0.9291 (mmm) REVERT: B 20 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8237 (mmmm) REVERT: B 30 ARG cc_start: 0.9475 (mtp85) cc_final: 0.8980 (mtp85) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1929 time to fit residues: 20.5438 Evaluate side-chains 72 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 569 GLN A 576 GLN A 660 ASN A 684 ASN A 712 GLN A 737 ASN A 759 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7285 Z= 0.226 Angle : 0.677 10.358 9875 Z= 0.338 Chirality : 0.040 0.132 1148 Planarity : 0.004 0.064 1291 Dihedral : 4.205 21.869 982 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.04 % Allowed : 27.22 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.29), residues: 915 helix: 0.66 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.40 (0.49), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 472 HIS 0.002 0.001 HIS A 706 PHE 0.015 0.001 PHE A 577 TYR 0.016 0.001 TYR A 482 ARG 0.003 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 472 TRP cc_start: 0.9320 (OUTLIER) cc_final: 0.8714 (m-90) REVERT: A 482 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.9001 (m-80) REVERT: B 30 ARG cc_start: 0.9496 (mtp85) cc_final: 0.9068 (mtp85) outliers start: 24 outliers final: 12 residues processed: 100 average time/residue: 0.1765 time to fit residues: 24.9179 Evaluate side-chains 90 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain B residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 68 optimal weight: 0.0770 chunk 56 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7285 Z= 0.171 Angle : 0.683 11.223 9875 Z= 0.326 Chirality : 0.040 0.185 1148 Planarity : 0.004 0.064 1291 Dihedral : 4.100 22.508 982 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.42 % Allowed : 26.33 % Favored : 70.25 % 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: 0.63 (0.29), residues: 915 helix: 0.72 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.35 (0.49), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 80 HIS 0.002 0.000 HIS A 145 PHE 0.013 0.001 PHE A 577 TYR 0.017 0.001 TYR A 482 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 TRP cc_start: 0.9244 (OUTLIER) cc_final: 0.8657 (m-90) REVERT: A 482 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8981 (m-80) REVERT: A 533 MET cc_start: 0.9184 (mmt) cc_final: 0.8860 (mmt) REVERT: A 608 MET cc_start: 0.8947 (tmm) cc_final: 0.8735 (ppp) REVERT: A 625 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.9011 (mt0) REVERT: A 788 MET cc_start: 0.9175 (mmm) cc_final: 0.8970 (mmm) REVERT: B 30 ARG cc_start: 0.9519 (mtp85) cc_final: 0.9115 (mtp85) outliers start: 27 outliers final: 13 residues processed: 105 average time/residue: 0.1905 time to fit residues: 27.4827 Evaluate side-chains 96 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.8285 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7285 Z= 0.202 Angle : 0.683 11.022 9875 Z= 0.331 Chirality : 0.041 0.213 1148 Planarity : 0.004 0.064 1291 Dihedral : 4.077 21.973 982 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.43 % Allowed : 26.33 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.83 (0.29), residues: 915 helix: 0.93 (0.20), residues: 711 sheet: None (None), residues: 0 loop : -0.51 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 430 HIS 0.002 0.001 HIS A 706 PHE 0.014 0.001 PHE A 577 TYR 0.018 0.001 TYR A 482 ARG 0.003 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.9498 (tt) cc_final: 0.9209 (pp) REVERT: A 252 MET cc_start: 0.9587 (mmm) cc_final: 0.9384 (mmm) REVERT: A 472 TRP cc_start: 0.9301 (OUTLIER) cc_final: 0.8719 (m-90) REVERT: A 482 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8965 (m-80) REVERT: A 588 LEU cc_start: 0.9401 (mm) cc_final: 0.9184 (mm) REVERT: A 625 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8937 (mt0) REVERT: A 719 ASP cc_start: 0.9052 (m-30) cc_final: 0.8670 (p0) REVERT: A 788 MET cc_start: 0.9259 (mmm) cc_final: 0.9032 (mmm) REVERT: B 20 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8536 (mttt) REVERT: B 30 ARG cc_start: 0.9528 (mtp85) cc_final: 0.9079 (mtp85) outliers start: 35 outliers final: 16 residues processed: 106 average time/residue: 0.1910 time to fit residues: 28.4007 Evaluate side-chains 96 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 0.0000 chunk 65 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7285 Z= 0.180 Angle : 0.691 11.722 9875 Z= 0.329 Chirality : 0.041 0.296 1148 Planarity : 0.004 0.061 1291 Dihedral : 4.016 21.987 982 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.42 % Allowed : 27.72 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.28), residues: 915 helix: 0.93 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.53 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.002 0.000 HIS A 706 PHE 0.014 0.001 PHE A 577 TYR 0.017 0.001 TYR A 482 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.9501 (tt) cc_final: 0.9235 (pp) REVERT: A 252 MET cc_start: 0.9607 (mmm) cc_final: 0.9207 (mmp) REVERT: A 408 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.9160 (pt0) REVERT: A 446 ASP cc_start: 0.9098 (t0) cc_final: 0.8678 (p0) REVERT: A 472 TRP cc_start: 0.9265 (OUTLIER) cc_final: 0.8748 (m-90) REVERT: A 482 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8954 (m-80) REVERT: A 533 MET cc_start: 0.9209 (mmt) cc_final: 0.8906 (mmt) REVERT: A 588 LEU cc_start: 0.9379 (mm) cc_final: 0.9079 (mm) REVERT: A 625 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8937 (mt0) REVERT: A 719 ASP cc_start: 0.9030 (m-30) cc_final: 0.8568 (p0) REVERT: A 788 MET cc_start: 0.9307 (mmm) cc_final: 0.9048 (mmm) REVERT: B 20 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8498 (mttt) REVERT: B 30 ARG cc_start: 0.9524 (mtp85) cc_final: 0.9118 (mtp85) outliers start: 27 outliers final: 17 residues processed: 100 average time/residue: 0.1766 time to fit residues: 24.6356 Evaluate side-chains 99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain B residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 88 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7285 Z= 0.228 Angle : 0.697 11.204 9875 Z= 0.339 Chirality : 0.040 0.220 1148 Planarity : 0.004 0.062 1291 Dihedral : 4.028 22.793 982 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.54 % Allowed : 27.85 % Favored : 68.61 % 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: 0.94 (0.29), residues: 915 helix: 0.98 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.37 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 80 HIS 0.003 0.001 HIS A 706 PHE 0.014 0.001 PHE A 577 TYR 0.019 0.001 TYR A 482 ARG 0.003 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8999 (mm) cc_final: 0.8723 (mm) REVERT: A 198 LEU cc_start: 0.9484 (tt) cc_final: 0.9259 (pp) REVERT: A 472 TRP cc_start: 0.9327 (OUTLIER) cc_final: 0.8755 (m-90) REVERT: A 482 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8935 (m-80) REVERT: A 588 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9107 (mm) REVERT: A 719 ASP cc_start: 0.9065 (m-30) cc_final: 0.8609 (p0) REVERT: A 788 MET cc_start: 0.9307 (mmm) cc_final: 0.9045 (mmm) REVERT: B 20 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8524 (mtmm) REVERT: B 30 ARG cc_start: 0.9505 (mtp85) cc_final: 0.9049 (mtp85) outliers start: 28 outliers final: 21 residues processed: 94 average time/residue: 0.1777 time to fit residues: 23.9675 Evaluate side-chains 98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain B residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.0170 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.0000 chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7285 Z= 0.176 Angle : 0.718 12.403 9875 Z= 0.339 Chirality : 0.041 0.193 1148 Planarity : 0.004 0.060 1291 Dihedral : 4.023 22.641 982 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.29 % Allowed : 28.86 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 915 helix: 0.99 (0.20), residues: 713 sheet: None (None), residues: 0 loop : -0.48 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 80 HIS 0.001 0.000 HIS A 706 PHE 0.012 0.001 PHE A 577 TYR 0.017 0.001 TYR A 482 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8978 (mm) cc_final: 0.8699 (mm) REVERT: A 198 LEU cc_start: 0.9452 (tt) cc_final: 0.9226 (pp) REVERT: A 290 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.9121 (mm-30) REVERT: A 408 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.9160 (pt0) REVERT: A 446 ASP cc_start: 0.9038 (t0) cc_final: 0.8758 (p0) REVERT: A 472 TRP cc_start: 0.9232 (OUTLIER) cc_final: 0.8871 (m-90) REVERT: A 482 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8997 (m-80) REVERT: A 533 MET cc_start: 0.9238 (mmt) cc_final: 0.8928 (mmm) REVERT: A 588 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9025 (mm) REVERT: A 625 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8689 (mm-40) REVERT: A 719 ASP cc_start: 0.8961 (m-30) cc_final: 0.8536 (p0) REVERT: A 788 MET cc_start: 0.9340 (mmm) cc_final: 0.9084 (mmm) REVERT: B 20 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8304 (mtmm) REVERT: B 30 ARG cc_start: 0.9527 (mtp85) cc_final: 0.9101 (mtp85) outliers start: 26 outliers final: 15 residues processed: 103 average time/residue: 0.1942 time to fit residues: 27.7532 Evaluate side-chains 100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 854 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 30.0000 chunk 68 optimal weight: 0.1980 chunk 79 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7285 Z= 0.174 Angle : 0.758 16.857 9875 Z= 0.352 Chirality : 0.041 0.225 1148 Planarity : 0.004 0.061 1291 Dihedral : 4.003 23.060 982 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.16 % Allowed : 29.49 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.28), residues: 915 helix: 0.99 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.46 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 80 HIS 0.001 0.000 HIS A 145 PHE 0.012 0.001 PHE A 577 TYR 0.015 0.001 TYR A 482 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8957 (mm) cc_final: 0.8661 (mm) REVERT: A 198 LEU cc_start: 0.9502 (tt) cc_final: 0.9301 (pp) REVERT: A 408 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.9168 (pt0) REVERT: A 446 ASP cc_start: 0.8977 (t0) cc_final: 0.8697 (p0) REVERT: A 472 TRP cc_start: 0.9253 (OUTLIER) cc_final: 0.8867 (m-90) REVERT: A 482 TYR cc_start: 0.9251 (OUTLIER) cc_final: 0.8974 (m-80) REVERT: A 533 MET cc_start: 0.9231 (mmt) cc_final: 0.9002 (mmt) REVERT: A 588 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9004 (mm) REVERT: A 625 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8611 (mm-40) REVERT: A 719 ASP cc_start: 0.8908 (m-30) cc_final: 0.8484 (p0) REVERT: A 788 MET cc_start: 0.9332 (mmm) cc_final: 0.9073 (mmm) REVERT: B 20 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8485 (mttt) REVERT: B 30 ARG cc_start: 0.9528 (mtp85) cc_final: 0.9112 (mtp85) outliers start: 25 outliers final: 17 residues processed: 97 average time/residue: 0.1843 time to fit residues: 24.8797 Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 854 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 10.0000 chunk 84 optimal weight: 0.0030 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7285 Z= 0.173 Angle : 0.763 15.278 9875 Z= 0.351 Chirality : 0.042 0.338 1148 Planarity : 0.004 0.059 1291 Dihedral : 3.930 23.106 982 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.04 % Allowed : 28.99 % Favored : 67.97 % 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: 1.02 (0.29), residues: 915 helix: 1.04 (0.20), residues: 713 sheet: None (None), residues: 0 loop : -0.38 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 80 HIS 0.001 0.000 HIS A 706 PHE 0.012 0.001 PHE A 36 TYR 0.016 0.001 TYR A 482 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8951 (mm) cc_final: 0.8662 (mm) REVERT: A 446 ASP cc_start: 0.8912 (t0) cc_final: 0.8667 (p0) REVERT: A 472 TRP cc_start: 0.9259 (OUTLIER) cc_final: 0.8897 (m-90) REVERT: A 482 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8969 (m-80) REVERT: A 533 MET cc_start: 0.9217 (mmt) cc_final: 0.9006 (mmt) REVERT: A 584 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9058 (mp) REVERT: A 588 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9032 (mm) REVERT: A 625 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8612 (mm-40) REVERT: A 719 ASP cc_start: 0.8921 (m-30) cc_final: 0.8436 (p0) REVERT: A 788 MET cc_start: 0.9349 (mmm) cc_final: 0.9096 (mmm) REVERT: B 20 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8491 (mttt) REVERT: B 30 ARG cc_start: 0.9528 (mtp85) cc_final: 0.9113 (mtp85) outliers start: 24 outliers final: 17 residues processed: 98 average time/residue: 0.1869 time to fit residues: 25.4604 Evaluate side-chains 103 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 854 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7285 Z= 0.209 Angle : 0.780 15.820 9875 Z= 0.363 Chirality : 0.042 0.327 1148 Planarity : 0.004 0.060 1291 Dihedral : 3.962 22.889 982 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.91 % Allowed : 29.37 % Favored : 67.72 % 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: 1.07 (0.29), residues: 915 helix: 1.08 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.37 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 80 HIS 0.003 0.001 HIS A 706 PHE 0.012 0.001 PHE A 577 TYR 0.019 0.001 TYR A 482 ARG 0.004 0.000 ARG B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8968 (mm) cc_final: 0.8683 (mm) REVERT: A 219 MET cc_start: 0.9182 (mmp) cc_final: 0.8896 (mtp) REVERT: A 446 ASP cc_start: 0.8940 (t0) cc_final: 0.8661 (p0) REVERT: A 472 TRP cc_start: 0.9307 (OUTLIER) cc_final: 0.8911 (m-90) REVERT: A 482 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8616 (m-80) REVERT: A 584 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 588 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9107 (mm) REVERT: A 625 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8622 (mm-40) REVERT: A 719 ASP cc_start: 0.8965 (m-30) cc_final: 0.8509 (p0) REVERT: A 788 MET cc_start: 0.9391 (mmm) cc_final: 0.9135 (mmm) REVERT: B 20 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8606 (mmtt) REVERT: B 30 ARG cc_start: 0.9518 (mtp85) cc_final: 0.9097 (mtp85) outliers start: 23 outliers final: 17 residues processed: 97 average time/residue: 0.1822 time to fit residues: 24.8762 Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 854 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.0070 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.056207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.041449 restraints weight = 50126.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.042852 restraints weight = 31993.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.043699 restraints weight = 23530.068| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7285 Z= 0.178 Angle : 0.780 16.482 9875 Z= 0.358 Chirality : 0.042 0.331 1148 Planarity : 0.004 0.059 1291 Dihedral : 3.961 24.091 982 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.66 % Allowed : 29.87 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 915 helix: 1.08 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.38 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 80 HIS 0.001 0.000 HIS A 706 PHE 0.010 0.001 PHE A 577 TYR 0.012 0.001 TYR A 482 ARG 0.006 0.000 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.71 seconds wall clock time: 28 minutes 11.75 seconds (1691.75 seconds total)