Starting phenix.real_space_refine on Fri Sep 11 19:44:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d1v_27138/09_2026/8d1v_27138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1v_27138/09_2026/8d1v_27138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d1v_27138/09_2026/8d1v_27138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1v_27138/09_2026/8d1v_27138.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d1v_27138/09_2026/8d1v_27138.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d1v_27138/09_2026/8d1v_27138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d1v_27138/09_2026/8d1v_27138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1v_27138/09_2026/8d1v_27138.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 51 5.49 5 S 47 5.16 5 C 6729 2.51 5 N 1965 2.21 5 O 2177 1.98 5 H 9 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10982 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1229, 9875 Classifications: {'peptide': 1229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 4, 'PTRANS': 69, 'TRANS': 1155} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 716 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 19, 'rna3p': 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 387 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 11} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7389 SG CYS A 965 52.610 79.489 34.405 1.00 16.18 S ATOM 7646 SG CYS A1312 54.788 76.398 34.787 1.00 42.26 S ATOM 7776 SG CYS A1342 56.145 79.835 35.770 1.00 16.46 S ATOM 7794 SG CYS A1345 53.703 78.265 37.918 1.00 42.76 S ATOM 5323 SG CYS A 706 67.274 57.736 63.303 1.00 64.50 S ATOM 5338 SG CYS A 708 66.711 61.546 63.496 1.00 47.76 S ATOM 5360 SG CYS A 711 63.819 58.979 64.304 1.00 40.08 S ATOM 3404 SG CYS A 463 56.018 42.763 85.262 1.00 49.22 S ATOM 3466 SG CYS A 472 56.667 39.772 87.611 1.00 43.87 S ATOM 3480 SG CYS A 474 56.786 43.428 88.933 1.00 31.88 S ATOM 3502 SG CYS A 477 53.532 41.954 87.701 1.00 37.68 S ATOM 704 SG CYS A 86 41.398 20.116 105.052 1.00 54.15 S ATOM 950 SG CYS A 115 39.201 17.399 106.531 1.00 59.03 S ATOM 1012 SG CYS A 123 37.966 21.095 106.260 1.00 59.56 S ATOM 1036 SG CYS A 126 38.414 19.054 103.155 1.00 54.26 S Time building chain proxies: 2.38, per 1000 atoms: 0.22 Number of scatterers: 10982 At special positions: 0 Unit cell: (84.66, 126.99, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 47 16.00 P 51 15.00 O 2177 8.00 N 1965 7.00 C 6729 6.00 H 9 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 411.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 965 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1342 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 706 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 708 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 472 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 115 " Number of angles added : 21 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 17 sheets defined 30.8% alpha, 25.1% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.990A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 260 through 276 removed outlier: 3.678A pdb=" N ALA A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 344 through 366 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 removed outlier: 3.585A pdb=" N THR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.431A pdb=" N GLU A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.578A pdb=" N ALA A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.839A pdb=" N ILE A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.559A pdb=" N ARG A 924 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.712A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1331 through 1336 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 3.604A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1476 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1535 Processing helix chain 'A' and resid 1538 through 1549 Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1582 removed outlier: 3.872A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1594 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.807A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 169 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.138A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.992A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.992A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA8, first strand: chain 'A' and resid 497 through 504 removed outlier: 5.593A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.557A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.557A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 744 removed outlier: 6.310A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 836 through 837 removed outlier: 6.943A pdb=" N ALA A 836 " --> pdb=" O TRP A1512 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN A1514 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.411A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB6, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.284A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.952A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLU A1446 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG A1443 " --> pdb=" O LEU A1388 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 9 1.05 - 1.24: 1339 1.24 - 1.43: 3607 1.43 - 1.62: 6313 1.62 - 1.81: 68 Bond restraints: 11336 Sorted by residual: bond pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 1.492 1.095 0.397 5.00e-02 4.00e+02 6.31e+01 bond pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.473 1.384 0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 1.533 1.606 -0.073 1.47e-02 4.63e+03 2.46e+01 bond pdb=" CB ASP A1536 " pdb=" CG ASP A1536 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.69e+00 bond pdb=" C3' C N 8 " pdb=" O3' C N 8 " ideal model delta sigma weight residual 1.415 1.441 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 11331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 15482 4.87 - 9.75: 37 9.75 - 14.62: 2 14.62 - 19.50: 2 19.50 - 24.37: 3 Bond angle restraints: 15526 Sorted by residual: angle pdb=" CA PRO A 114 " pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 112.00 87.63 24.37 1.40e+00 5.10e-01 3.03e+02 angle pdb=" N PRO A 114 " pdb=" CD PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 103.20 86.02 17.18 1.50e+00 4.44e-01 1.31e+02 angle pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 104.50 84.08 20.42 1.90e+00 2.77e-01 1.16e+02 angle pdb=" C GLU A 877 " pdb=" N GLU A 878 " pdb=" CA GLU A 878 " ideal model delta sigma weight residual 121.70 136.07 -14.37 1.80e+00 3.09e-01 6.37e+01 angle pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 106.10 88.47 17.63 3.20e+00 9.77e-02 3.04e+01 ... (remaining 15521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6508 35.97 - 71.94: 233 71.94 - 107.90: 24 107.90 - 143.87: 0 143.87 - 179.84: 2 Dihedral angle restraints: 6767 sinusoidal: 3238 harmonic: 3529 Sorted by residual: dihedral pdb=" C4' A J 14 " pdb=" C3' A J 14 " pdb=" C2' A J 14 " pdb=" C1' A J 14 " ideal model delta sinusoidal sigma weight residual 36.34 -39.59 75.93 1 3.10e+00 1.04e-01 7.56e+02 dihedral pdb=" C4' G J 6 " pdb=" C3' G J 6 " pdb=" C2' G J 6 " pdb=" C1' G J 6 " ideal model delta sinusoidal sigma weight residual 36.35 -38.94 75.28 1 3.10e+00 1.04e-01 7.45e+02 dihedral pdb=" C4' C N 22 " pdb=" C3' C N 22 " pdb=" C2' C N 22 " pdb=" C1' C N 22 " ideal model delta sinusoidal sigma weight residual 36.35 -38.88 75.23 1 3.10e+00 1.04e-01 7.44e+02 ... (remaining 6764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1455 0.080 - 0.161: 120 0.161 - 0.241: 49 0.241 - 0.321: 44 0.321 - 0.402: 5 Chirality restraints: 1673 Sorted by residual: chirality pdb=" C2' C N 22 " pdb=" C3' C N 22 " pdb=" O2' C N 22 " pdb=" C1' C N 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.39 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" P U N 9 " pdb=" OP1 U N 9 " pdb=" OP2 U N 9 " pdb=" O5' U N 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C3' A J 14 " pdb=" C4' A J 14 " pdb=" O3' A J 14 " pdb=" C2' A J 14 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 1670 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 113 " -0.062 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 114 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U J 24 " -0.032 2.00e-02 2.50e+03 1.72e-02 6.66e+00 pdb=" N1 U J 24 " 0.036 2.00e-02 2.50e+03 pdb=" C2 U J 24 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U J 24 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U J 24 " 0.009 2.00e-02 2.50e+03 pdb=" C4 U J 24 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U J 24 " -0.013 2.00e-02 2.50e+03 pdb=" C5 U J 24 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U J 24 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 825 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ASP A 825 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP A 825 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 826 " 0.011 2.00e-02 2.50e+03 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.57: 143 2.57 - 3.08: 7593 3.08 - 3.58: 13373 3.58 - 4.09: 21124 4.09 - 4.60: 30889 Nonbonded interactions: 73122 Sorted by model distance: nonbonded pdb=" O SER A 399 " pdb=" OG SER A 583 " model vdw 2.059 2.800 nonbonded pdb=" OD2 ASP A 193 " pdb=" OG1 THR A 195 " model vdw 2.063 2.800 nonbonded pdb=" OH TYR A 863 " pdb=" OP2 A J 30 " model vdw 2.178 2.800 nonbonded pdb=" NE ARG A 951 " pdb=" OP1 U J 24 " model vdw 2.195 2.950 nonbonded pdb=" O GLY A1486 " pdb=" NZ LYS A1489 " model vdw 2.199 2.950 ... (remaining 73117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.006 0.397 11343 Z= 0.238 Angle : 0.863 24.374 15528 Z= 0.431 Chirality : 0.074 0.402 1673 Planarity : 0.005 0.082 1829 Dihedral : 17.672 179.839 4489 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1217 helix: -0.15 (0.28), residues: 318 sheet: -0.09 (0.35), residues: 206 loop : -0.47 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.015 0.002 TYR A 577 PHE 0.020 0.002 PHE A 757 TRP 0.015 0.001 TRP A 597 HIS 0.010 0.001 HIS A 931 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.24 (11327) covalent geometry : angle 0.85503 / 0.43 (15507) hydrogen bonds : bond 0.23799 / 15.68 ( 364) hydrogen bonds : angle 8.82194 / 6.03 ( 1097) metal coordination : bond 0.00820 / 0.48 ( 16) metal coordination : angle 3.36015 / 1.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7569 (mt) cc_final: 0.7329 (mp) REVERT: A 188 LYS cc_start: 0.7473 (ptpt) cc_final: 0.7017 (mtmt) REVERT: A 209 LYS cc_start: 0.5970 (pttm) cc_final: 0.5489 (pttp) REVERT: A 294 ARG cc_start: 0.7611 (ptt-90) cc_final: 0.7201 (ptt90) REVERT: A 473 MET cc_start: 0.7444 (mmm) cc_final: 0.7197 (mmt) REVERT: A 507 PHE cc_start: 0.7649 (m-80) cc_final: 0.7398 (m-10) REVERT: A 589 ASN cc_start: 0.7330 (m-40) cc_final: 0.6445 (m-40) REVERT: A 616 GLU cc_start: 0.6167 (tp30) cc_final: 0.5666 (tt0) REVERT: A 786 GLU cc_start: 0.6700 (pm20) cc_final: 0.6488 (pm20) REVERT: A 970 ASP cc_start: 0.6937 (p0) cc_final: 0.6725 (p0) REVERT: A 1566 LYS cc_start: 0.7675 (tttt) cc_final: 0.7301 (tttm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.7354 time to fit residues: 127.1024 Evaluate side-chains 97 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.180786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154198 restraints weight = 11260.527| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.41 r_work: 0.3667 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 11343 Z= 0.370 Angle : 1.310 28.363 15528 Z= 0.566 Chirality : 0.122 1.315 1673 Planarity : 0.007 0.055 1829 Dihedral : 16.447 175.251 1963 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 32.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.93 % Allowed : 10.30 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.24), residues: 1217 helix: 0.23 (0.29), residues: 313 sheet: 0.10 (0.35), residues: 211 loop : -0.83 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1565 TYR 0.024 0.003 TYR A 534 PHE 0.024 0.003 PHE A 757 TRP 0.016 0.003 TRP A1512 HIS 0.012 0.002 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.37 (11327) covalent geometry : angle 1.30098 / 0.57 (15507) hydrogen bonds : bond 0.06917 / 4.56 ( 364) hydrogen bonds : angle 6.27724 / 4.37 ( 1097) metal coordination : bond 0.01109 / 0.70 ( 16) metal coordination : angle 4.41601 / 2.08 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7623 (mt) cc_final: 0.7335 (mp) REVERT: A 188 LYS cc_start: 0.7539 (ptpt) cc_final: 0.7270 (mtmt) REVERT: A 209 LYS cc_start: 0.5835 (pttm) cc_final: 0.5373 (pttp) REVERT: A 294 ARG cc_start: 0.7628 (ptt-90) cc_final: 0.7303 (ttp-170) REVERT: A 341 GLU cc_start: 0.6589 (pm20) cc_final: 0.6355 (pm20) REVERT: A 409 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: A 473 MET cc_start: 0.7448 (mmm) cc_final: 0.7220 (mmt) REVERT: A 614 LEU cc_start: 0.7614 (tp) cc_final: 0.7315 (tt) REVERT: A 896 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7118 (ttp80) REVERT: A 1310 ARG cc_start: 0.6682 (tpp80) cc_final: 0.6467 (mmm-85) REVERT: A 1369 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 1375 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6124 (ttpt) REVERT: A 1395 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6991 (mmp80) REVERT: A 1478 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 1487 MET cc_start: 0.8561 (ptt) cc_final: 0.8127 (ptt) REVERT: A 1592 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7905 (mmtt) outliers start: 31 outliers final: 8 residues processed: 129 average time/residue: 0.6728 time to fit residues: 92.9846 Evaluate side-chains 110 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.186888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.161640 restraints weight = 11405.234| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.21 r_work: 0.3722 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11343 Z= 0.189 Angle : 0.864 14.095 15528 Z= 0.381 Chirality : 0.081 0.994 1673 Planarity : 0.005 0.050 1829 Dihedral : 17.190 178.627 1963 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 33.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.74 % Allowed : 13.80 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1217 helix: 0.85 (0.30), residues: 319 sheet: 0.16 (0.35), residues: 214 loop : -0.84 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.015 0.002 TYR A 534 PHE 0.015 0.002 PHE A 757 TRP 0.009 0.001 TRP A1466 HIS 0.006 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (11327) covalent geometry : angle 0.85695 / 0.38 (15507) hydrogen bonds : bond 0.05003 / 3.35 ( 364) hydrogen bonds : angle 5.46983 / 3.81 ( 1097) metal coordination : bond 0.00556 / 0.32 ( 16) metal coordination : angle 3.11191 / 1.43 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.7052 (tptm) REVERT: A 147 ARG cc_start: 0.6400 (ttp-170) cc_final: 0.6179 (ttp-170) REVERT: A 155 LEU cc_start: 0.7583 (mt) cc_final: 0.7378 (mp) REVERT: A 188 LYS cc_start: 0.7384 (ptpt) cc_final: 0.7139 (mtmt) REVERT: A 209 LYS cc_start: 0.5808 (pttm) cc_final: 0.5331 (pttp) REVERT: A 294 ARG cc_start: 0.7470 (ptt-90) cc_final: 0.7145 (ttp-170) REVERT: A 341 GLU cc_start: 0.6681 (pm20) cc_final: 0.6443 (pm20) REVERT: A 395 VAL cc_start: 0.6548 (OUTLIER) cc_final: 0.6094 (m) REVERT: A 409 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: A 473 MET cc_start: 0.7460 (mmm) cc_final: 0.7218 (mmt) REVERT: A 503 ARG cc_start: 0.7343 (ttp-170) cc_final: 0.7071 (ttt180) REVERT: A 627 GLU cc_start: 0.8140 (tt0) cc_final: 0.7767 (tt0) REVERT: A 664 GLU cc_start: 0.6186 (tp30) cc_final: 0.5843 (tp30) REVERT: A 735 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.5120 (pp20) REVERT: A 970 ASP cc_start: 0.7233 (p0) cc_final: 0.6802 (p0) REVERT: A 1305 MET cc_start: 0.6534 (ptp) cc_final: 0.6274 (ptp) REVERT: A 1369 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 1375 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.5997 (ttpt) REVERT: A 1395 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6846 (mmp80) REVERT: A 1405 ASN cc_start: 0.6413 (m-40) cc_final: 0.6156 (m-40) REVERT: A 1478 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: A 1487 MET cc_start: 0.8476 (ptt) cc_final: 0.8048 (ptt) outliers start: 29 outliers final: 7 residues processed: 130 average time/residue: 0.7570 time to fit residues: 104.8735 Evaluate side-chains 117 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.182270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156021 restraints weight = 11316.860| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.38 r_work: 0.3664 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11343 Z= 0.312 Angle : 1.040 14.494 15528 Z= 0.463 Chirality : 0.089 0.857 1673 Planarity : 0.006 0.052 1829 Dihedral : 17.203 177.240 1963 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 34.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 4.06 % Allowed : 15.12 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1217 helix: 0.33 (0.29), residues: 313 sheet: 0.01 (0.35), residues: 211 loop : -1.02 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 25 TYR 0.021 0.003 TYR A 534 PHE 0.021 0.003 PHE A 757 TRP 0.012 0.002 TRP A1512 HIS 0.010 0.002 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.31 (11327) covalent geometry : angle 1.03035 / 0.46 (15507) hydrogen bonds : bond 0.05799 / 3.82 ( 364) hydrogen bonds : angle 5.80303 / 4.05 ( 1097) metal coordination : bond 0.00797 / 0.44 ( 16) metal coordination : angle 3.88815 / 1.88 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.414 Fit side-chains REVERT: A 46 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7013 (tptm) REVERT: A 155 LEU cc_start: 0.7655 (mt) cc_final: 0.7427 (mp) REVERT: A 173 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8099 (mt) REVERT: A 188 LYS cc_start: 0.7497 (ptpt) cc_final: 0.7234 (mtmt) REVERT: A 209 LYS cc_start: 0.5781 (pttm) cc_final: 0.5317 (pttp) REVERT: A 293 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7176 (ptm-80) REVERT: A 341 GLU cc_start: 0.6765 (pm20) cc_final: 0.6424 (pm20) REVERT: A 409 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: A 473 MET cc_start: 0.7639 (mmm) cc_final: 0.7298 (mmt) REVERT: A 503 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7213 (ttt180) REVERT: A 524 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: A 627 GLU cc_start: 0.8167 (tt0) cc_final: 0.7963 (tt0) REVERT: A 664 GLU cc_start: 0.6119 (tp30) cc_final: 0.5528 (pt0) REVERT: A 667 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.5079 (pt0) REVERT: A 707 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5746 (tt0) REVERT: A 735 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5396 (pp20) REVERT: A 855 ARG cc_start: 0.7133 (mmp-170) cc_final: 0.6929 (mpp-170) REVERT: A 896 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: A 970 ASP cc_start: 0.7375 (p0) cc_final: 0.6930 (p0) REVERT: A 1369 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: A 1375 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.6034 (ttpt) REVERT: A 1395 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7046 (mmp80) REVERT: A 1405 ASN cc_start: 0.6360 (m-40) cc_final: 0.6063 (m-40) REVERT: A 1478 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: A 1487 MET cc_start: 0.8479 (ptt) cc_final: 0.8131 (ptt) REVERT: A 1532 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: A 1592 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7721 (mmtt) outliers start: 43 outliers final: 17 residues processed: 137 average time/residue: 0.7363 time to fit residues: 107.5150 Evaluate side-chains 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain A residue 1532 GLU Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 0.0270 chunk 122 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 0.0570 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.187733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162038 restraints weight = 11191.356| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.41 r_work: 0.3745 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11343 Z= 0.135 Angle : 0.749 12.805 15528 Z= 0.330 Chirality : 0.066 0.563 1673 Planarity : 0.004 0.050 1829 Dihedral : 16.889 177.200 1963 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 34.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 2.36 % Allowed : 17.30 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1217 helix: 1.09 (0.30), residues: 321 sheet: 0.16 (0.35), residues: 214 loop : -0.83 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 102 TYR 0.011 0.001 TYR A 534 PHE 0.013 0.001 PHE A 757 TRP 0.009 0.001 TRP A1466 HIS 0.004 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11327) covalent geometry : angle 0.74338 / 0.33 (15507) hydrogen bonds : bond 0.04052 / 2.69 ( 364) hydrogen bonds : angle 5.01506 / 3.51 ( 1097) metal coordination : bond 0.00387 / 0.21 ( 16) metal coordination : angle 2.51428 / 1.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.313 Fit side-chains REVERT: A 188 LYS cc_start: 0.7425 (ptpt) cc_final: 0.7221 (mtmt) REVERT: A 209 LYS cc_start: 0.5791 (pttm) cc_final: 0.5332 (pttp) REVERT: A 293 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7120 (ptm-80) REVERT: A 294 ARG cc_start: 0.7363 (ptt-90) cc_final: 0.7079 (ttp-170) REVERT: A 341 GLU cc_start: 0.6663 (pm20) cc_final: 0.6333 (pm20) REVERT: A 401 LEU cc_start: 0.6661 (tp) cc_final: 0.6449 (tp) REVERT: A 473 MET cc_start: 0.7540 (mmm) cc_final: 0.7049 (mmt) REVERT: A 576 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7499 (mtpt) REVERT: A 627 GLU cc_start: 0.8137 (tt0) cc_final: 0.7920 (tt0) REVERT: A 664 GLU cc_start: 0.6061 (tp30) cc_final: 0.5602 (pt0) REVERT: A 735 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5140 (pp20) REVERT: A 855 ARG cc_start: 0.7142 (mmp-170) cc_final: 0.6929 (mpp-170) REVERT: A 970 ASP cc_start: 0.7162 (p0) cc_final: 0.6732 (p0) REVERT: A 1363 SER cc_start: 0.8420 (m) cc_final: 0.8208 (m) REVERT: A 1369 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 1395 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6988 (mmp80) REVERT: A 1487 MET cc_start: 0.8412 (ptt) cc_final: 0.8051 (ptt) outliers start: 25 outliers final: 9 residues processed: 128 average time/residue: 0.7148 time to fit residues: 97.6435 Evaluate side-chains 115 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1395 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 109 optimal weight: 0.0980 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.0020 chunk 47 optimal weight: 0.5980 overall best weight: 2.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.185297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159334 restraints weight = 11224.304| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.43 r_work: 0.3717 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11343 Z= 0.219 Angle : 0.851 13.084 15528 Z= 0.378 Chirality : 0.073 0.675 1673 Planarity : 0.005 0.051 1829 Dihedral : 16.925 178.510 1963 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 34.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.93 % Rotamer: Outliers : 3.40 % Allowed : 16.54 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1217 helix: 0.88 (0.30), residues: 315 sheet: 0.14 (0.35), residues: 209 loop : -0.89 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1310 TYR 0.017 0.002 TYR A 534 PHE 0.017 0.002 PHE A 757 TRP 0.010 0.002 TRP A1466 HIS 0.007 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (11327) covalent geometry : angle 0.84422 / 0.38 (15507) hydrogen bonds : bond 0.04720 / 3.13 ( 364) hydrogen bonds : angle 5.28220 / 3.70 ( 1097) metal coordination : bond 0.00491 / 0.26 ( 16) metal coordination : angle 2.96144 / 1.43 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.416 Fit side-chains REVERT: A 155 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7413 (mp) REVERT: A 173 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8185 (mt) REVERT: A 188 LYS cc_start: 0.7414 (ptpt) cc_final: 0.7188 (mtmt) REVERT: A 209 LYS cc_start: 0.5721 (pttm) cc_final: 0.5252 (pttp) REVERT: A 293 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7133 (ptm-80) REVERT: A 294 ARG cc_start: 0.7301 (ptt-90) cc_final: 0.7039 (ttp-170) REVERT: A 298 LEU cc_start: 0.6096 (mt) cc_final: 0.5564 (mt) REVERT: A 341 GLU cc_start: 0.6719 (pm20) cc_final: 0.6351 (pm20) REVERT: A 395 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.5922 (m) REVERT: A 409 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: A 473 MET cc_start: 0.7622 (mmm) cc_final: 0.7274 (mmt) REVERT: A 524 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: A 664 GLU cc_start: 0.6048 (tp30) cc_final: 0.5594 (pt0) REVERT: A 707 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5493 (tt0) REVERT: A 735 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5248 (pp20) REVERT: A 855 ARG cc_start: 0.7148 (mmp-170) cc_final: 0.6894 (mpp-170) REVERT: A 970 ASP cc_start: 0.7236 (p0) cc_final: 0.6858 (p0) REVERT: A 1369 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: A 1375 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.6040 (ttpt) REVERT: A 1395 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6867 (mmp80) REVERT: A 1487 MET cc_start: 0.8453 (ptt) cc_final: 0.8127 (ptt) REVERT: A 1579 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6333 (mp) outliers start: 36 outliers final: 12 residues processed: 131 average time/residue: 0.7040 time to fit residues: 98.4209 Evaluate side-chains 124 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1579 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.185368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159297 restraints weight = 11174.214| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.36 r_work: 0.3705 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11343 Z= 0.206 Angle : 0.835 12.942 15528 Z= 0.372 Chirality : 0.071 0.675 1673 Planarity : 0.005 0.051 1829 Dihedral : 16.892 178.924 1963 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 34.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.26 % Rotamer: Outliers : 3.69 % Allowed : 17.01 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1217 helix: 0.89 (0.30), residues: 315 sheet: 0.12 (0.35), residues: 209 loop : -0.91 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1310 TYR 0.016 0.002 TYR A 534 PHE 0.016 0.002 PHE A 757 TRP 0.010 0.001 TRP A1466 HIS 0.007 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (11327) covalent geometry : angle 0.82921 / 0.37 (15507) hydrogen bonds : bond 0.04618 / 3.05 ( 364) hydrogen bonds : angle 5.22368 / 3.66 ( 1097) metal coordination : bond 0.00498 / 0.27 ( 16) metal coordination : angle 2.85860 / 1.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.356 Fit side-chains REVERT: A 17 MET cc_start: 0.8300 (ttp) cc_final: 0.8049 (ttp) REVERT: A 173 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 188 LYS cc_start: 0.7438 (ptpt) cc_final: 0.7229 (mtmt) REVERT: A 209 LYS cc_start: 0.5720 (pttm) cc_final: 0.5264 (pttp) REVERT: A 293 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7193 (ptm-80) REVERT: A 294 ARG cc_start: 0.7261 (ptt-90) cc_final: 0.7030 (ttp-170) REVERT: A 341 GLU cc_start: 0.6653 (pm20) cc_final: 0.6292 (pm20) REVERT: A 409 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: A 473 MET cc_start: 0.7615 (mmm) cc_final: 0.7275 (mmt) REVERT: A 524 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: A 664 GLU cc_start: 0.6173 (tp30) cc_final: 0.5755 (pt0) REVERT: A 707 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5551 (tt0) REVERT: A 735 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.5241 (pp20) REVERT: A 855 ARG cc_start: 0.7242 (mmp-170) cc_final: 0.6957 (mpp-170) REVERT: A 970 ASP cc_start: 0.7280 (p0) cc_final: 0.6924 (p0) REVERT: A 1305 MET cc_start: 0.6478 (ptp) cc_final: 0.6176 (ptp) REVERT: A 1369 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: A 1375 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5929 (ttpt) REVERT: A 1395 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6965 (mmp80) REVERT: A 1478 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: A 1487 MET cc_start: 0.8462 (ptt) cc_final: 0.8149 (ptt) REVERT: A 1579 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6438 (mp) outliers start: 39 outliers final: 16 residues processed: 134 average time/residue: 0.6662 time to fit residues: 95.5883 Evaluate side-chains 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain A residue 1579 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.182800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.157144 restraints weight = 11222.574| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.22 r_work: 0.3676 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11343 Z= 0.329 Angle : 1.030 14.495 15528 Z= 0.462 Chirality : 0.086 0.870 1673 Planarity : 0.006 0.050 1829 Dihedral : 17.227 178.792 1963 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 35.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.63 % Favored : 91.21 % Rotamer: Outliers : 3.50 % Allowed : 18.15 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.23), residues: 1217 helix: 0.32 (0.29), residues: 313 sheet: -0.10 (0.35), residues: 215 loop : -1.15 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1310 TYR 0.021 0.003 TYR A 534 PHE 0.019 0.003 PHE A 757 TRP 0.013 0.002 TRP A1512 HIS 0.010 0.002 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.33 (11327) covalent geometry : angle 1.02195 / 0.46 (15507) hydrogen bonds : bond 0.05635 / 3.69 ( 364) hydrogen bonds : angle 5.76179 / 4.03 ( 1097) metal coordination : bond 0.00699 / 0.37 ( 16) metal coordination : angle 3.70243 / 1.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.321 Fit side-chains REVERT: A 155 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 173 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8256 (mt) REVERT: A 188 LYS cc_start: 0.7431 (ptpt) cc_final: 0.7163 (mtmt) REVERT: A 209 LYS cc_start: 0.5745 (pttm) cc_final: 0.5274 (pttp) REVERT: A 293 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7199 (ptm-80) REVERT: A 298 LEU cc_start: 0.6009 (mt) cc_final: 0.5463 (mt) REVERT: A 409 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: A 473 MET cc_start: 0.7647 (mmm) cc_final: 0.7274 (mmm) REVERT: A 524 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: A 664 GLU cc_start: 0.6131 (tp30) cc_final: 0.5661 (pt0) REVERT: A 707 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5753 (tt0) REVERT: A 735 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5618 (pp20) REVERT: A 832 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 929 GLU cc_start: 0.6618 (tt0) cc_final: 0.6241 (tt0) REVERT: A 970 ASP cc_start: 0.7330 (p0) cc_final: 0.6927 (p0) REVERT: A 1305 MET cc_start: 0.6575 (ptp) cc_final: 0.6181 (ptp) REVERT: A 1369 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: A 1375 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5927 (ttpt) REVERT: A 1395 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7107 (mmp80) REVERT: A 1478 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: A 1487 MET cc_start: 0.8470 (ptt) cc_final: 0.8239 (ptt) REVERT: A 1579 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6542 (mp) REVERT: A 1592 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7807 (mmtt) outliers start: 37 outliers final: 21 residues processed: 128 average time/residue: 0.6161 time to fit residues: 84.6716 Evaluate side-chains 128 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.0370 chunk 31 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 3.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 712 GLN A 887 HIS A1405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.185773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160392 restraints weight = 11184.923| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.30 r_work: 0.3730 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11343 Z= 0.234 Angle : 0.888 13.821 15528 Z= 0.396 Chirality : 0.075 0.744 1673 Planarity : 0.005 0.049 1829 Dihedral : 16.943 179.587 1963 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 35.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.31 % Favored : 92.52 % Rotamer: Outliers : 3.50 % Allowed : 18.43 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.23), residues: 1217 helix: 0.57 (0.30), residues: 313 sheet: -0.03 (0.35), residues: 209 loop : -1.12 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1310 TYR 0.018 0.002 TYR A 534 PHE 0.018 0.002 PHE A 757 TRP 0.012 0.002 TRP A1466 HIS 0.007 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (11327) covalent geometry : angle 0.88077 / 0.40 (15507) hydrogen bonds : bond 0.04884 / 3.21 ( 364) hydrogen bonds : angle 5.42641 / 3.79 ( 1097) metal coordination : bond 0.00545 / 0.28 ( 16) metal coordination : angle 3.13354 / 1.59 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 173 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 209 LYS cc_start: 0.5731 (pttm) cc_final: 0.5247 (pttp) REVERT: A 293 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7205 (ptm-80) REVERT: A 473 MET cc_start: 0.7582 (mmm) cc_final: 0.7135 (mmt) REVERT: A 524 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: A 590 ASP cc_start: 0.7148 (p0) cc_final: 0.6317 (m-30) REVERT: A 664 GLU cc_start: 0.6137 (tp30) cc_final: 0.5706 (pt0) REVERT: A 707 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5492 (tt0) REVERT: A 735 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5760 (pp20) REVERT: A 832 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 929 GLU cc_start: 0.6554 (tt0) cc_final: 0.6137 (tt0) REVERT: A 970 ASP cc_start: 0.7287 (p0) cc_final: 0.6962 (p0) REVERT: A 1305 MET cc_start: 0.6499 (ptp) cc_final: 0.6133 (ptp) REVERT: A 1369 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: A 1375 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5876 (ttpt) REVERT: A 1395 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6954 (mmp80) REVERT: A 1478 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: A 1579 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6465 (mp) REVERT: A 1592 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7722 (mmtt) outliers start: 37 outliers final: 18 residues processed: 130 average time/residue: 0.5997 time to fit residues: 83.9445 Evaluate side-chains 127 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1592 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 887 HIS A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.187530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161342 restraints weight = 11332.931| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.51 r_work: 0.3733 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11343 Z= 0.157 Angle : 0.746 11.834 15528 Z= 0.334 Chirality : 0.064 0.585 1673 Planarity : 0.004 0.050 1829 Dihedral : 16.610 179.632 1963 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 35.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.43 % Rotamer: Outliers : 2.93 % Allowed : 18.90 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1217 helix: 1.07 (0.30), residues: 315 sheet: 0.11 (0.36), residues: 209 loop : -0.92 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1310 TYR 0.012 0.002 TYR A 534 PHE 0.014 0.001 PHE A 757 TRP 0.013 0.001 TRP A1466 HIS 0.005 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (11327) covalent geometry : angle 0.74122 / 0.33 (15507) hydrogen bonds : bond 0.04151 / 2.74 ( 364) hydrogen bonds : angle 5.00380 / 3.50 ( 1097) metal coordination : bond 0.00405 / 0.24 ( 16) metal coordination : angle 2.41343 / 1.19 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.338 Fit side-chains REVERT: A 17 MET cc_start: 0.8257 (ttp) cc_final: 0.8027 (ttp) REVERT: A 173 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8223 (mt) REVERT: A 209 LYS cc_start: 0.5768 (pttm) cc_final: 0.5307 (pttp) REVERT: A 293 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7228 (ptm-80) REVERT: A 341 GLU cc_start: 0.6659 (pm20) cc_final: 0.6272 (pm20) REVERT: A 401 LEU cc_start: 0.6604 (tp) cc_final: 0.6394 (tp) REVERT: A 473 MET cc_start: 0.7614 (mmm) cc_final: 0.7253 (mmt) REVERT: A 524 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: A 576 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7531 (mtpt) REVERT: A 580 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7104 (mt) REVERT: A 590 ASP cc_start: 0.7087 (p0) cc_final: 0.6283 (m-30) REVERT: A 664 GLU cc_start: 0.6128 (tp30) cc_final: 0.5703 (pt0) REVERT: A 666 GLU cc_start: 0.6392 (tt0) cc_final: 0.6003 (mt-10) REVERT: A 832 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 929 GLU cc_start: 0.6464 (tt0) cc_final: 0.6064 (tt0) REVERT: A 970 ASP cc_start: 0.7207 (p0) cc_final: 0.6497 (p0) REVERT: A 1305 MET cc_start: 0.6486 (ptp) cc_final: 0.6194 (ptp) REVERT: A 1363 SER cc_start: 0.8442 (m) cc_final: 0.8240 (m) REVERT: A 1369 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: A 1375 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.5927 (ttpt) REVERT: A 1395 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6942 (mmp80) REVERT: A 1478 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7268 (mt-10) outliers start: 31 outliers final: 18 residues processed: 131 average time/residue: 0.5969 time to fit residues: 84.2060 Evaluate side-chains 129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1375 LYS Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1478 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 887 HIS A1405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.188641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162970 restraints weight = 11256.743| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.36 r_work: 0.3756 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11343 Z= 0.141 Angle : 0.705 11.059 15528 Z= 0.318 Chirality : 0.060 0.460 1673 Planarity : 0.004 0.050 1829 Dihedral : 16.444 179.437 1963 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 35.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 2.74 % Allowed : 19.28 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1217 helix: 1.30 (0.30), residues: 321 sheet: 0.18 (0.35), residues: 214 loop : -0.80 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1310 TYR 0.013 0.002 TYR A 534 PHE 0.013 0.001 PHE A 757 TRP 0.012 0.001 TRP A 20 HIS 0.004 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (11327) covalent geometry : angle 0.70135 / 0.32 (15507) hydrogen bonds : bond 0.04006 / 2.65 ( 364) hydrogen bonds : angle 4.84408 / 3.40 ( 1097) metal coordination : bond 0.00344 / 0.19 ( 16) metal coordination : angle 2.18510 / 1.11 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3699.08 seconds wall clock time: 64 minutes 3.15 seconds (3843.15 seconds total)