Starting phenix.real_space_refine on Fri Jul 3 01:22:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y81_33677/07_2026/7y81_33677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y81_33677/07_2026/7y81_33677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2026/7y81_33677.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2026/7y81_33677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2026/7y81_33677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2026/7y81_33677.map" model { file = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2026/7y81_33677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2026/7y81_33677.cif" } resolution = 2.54 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= 0.280 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 55 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 6810 2.51 5 N 1927 2.21 5 O 2216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11044 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9871 Classifications: {'peptide': 1223} Link IDs: {'PTRANS': 57, 'TRANS': 1165} Chain breaks: 9 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1, ' ZN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5559 SG CYS A 750 16.364 55.912 74.661 1.00 60.87 S ATOM 5572 SG CYS A 752 19.374 57.335 76.428 1.00 46.81 S ATOM 5594 SG CYS A 755 19.800 54.173 74.505 1.00 46.28 S ATOM 3484 SG CYS A 491 27.123 52.899 47.829 1.00 56.05 S ATOM 3552 SG CYS A 501 27.375 53.613 44.369 1.00 42.85 S ATOM 3566 SG CYS A 503 29.995 55.155 46.413 1.00 43.99 S ATOM 3588 SG CYS A 506 30.124 51.342 46.034 1.00 41.71 S ATOM 7485 SG CYS A1018 19.155 40.566 107.931 1.00 37.91 S ATOM 7681 SG CYS A1406 16.821 41.452 105.025 1.00 27.11 S ATOM 7732 SG CYS A1414 18.500 44.019 107.321 1.00 29.63 S ATOM 7749 SG CYS A1417 20.643 42.384 104.854 1.00 46.17 S ATOM 668 SG CYS A 88 36.834 43.752 17.551 1.00 58.67 S ATOM 939 SG CYS A 121 37.795 41.575 14.500 1.00 73.50 S ATOM 985 SG CYS A 127 39.732 41.241 17.690 1.00 55.95 S ATOM 1009 SG CYS A 130 36.159 40.052 17.526 1.00 59.89 S Time building chain proxies: 2.03, per 1000 atoms: 0.18 Number of scatterers: 11044 At special positions: 0 Unit cell: (75.9, 81.4, 156.2, 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 31 16.00 P 55 15.00 Mg 1 11.99 O 2216 8.00 N 1927 7.00 C 6810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 486.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1406 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 88 " Number of angles added : 21 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 19 sheets defined 31.0% alpha, 26.7% beta 13 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.293A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.610A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 269 through 287 removed outlier: 3.550A pdb=" N ASN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 4.359A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 373 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.501A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 624 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 658 through 664 removed outlier: 3.953A pdb=" N GLU A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.715A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.539A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.697A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.960A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 Processing helix chain 'A' and resid 1493 through 1501 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.924A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.581A pdb=" N LYS A1593 " --> pdb=" O GLU A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.632A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1667 Processing helix chain 'A' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.883A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.774A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.511A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.637A pdb=" N VAL A 85 " --> pdb=" O TRP A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 5.912A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.206A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.206A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.526A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 533 removed outlier: 10.417A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.713A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.713A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.192A pdb=" N ILE A 700 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 803 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB5, first strand: chain 'A' and resid 1642 through 1643 removed outlier: 6.746A pdb=" N ILE A 920 " --> pdb=" O TRP A1688 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.264A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA A1434 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASP A1521 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR A1436 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER A1519 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A1438 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 5.260A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU A1567 " --> pdb=" O VAL A1582 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.168A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 989 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1421 through 1422 390 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1874 1.32 - 1.44: 3281 1.44 - 1.57: 6103 1.57 - 1.69: 104 1.69 - 1.81: 42 Bond restraints: 11404 Sorted by residual: bond pdb=" O3' U B 34 " pdb=" P A B 35 " ideal model delta sigma weight residual 1.607 1.514 0.093 1.50e-02 4.44e+03 3.84e+01 bond pdb=" O3' C B 45 " pdb=" P U B 46 " ideal model delta sigma weight residual 1.607 1.521 0.086 1.50e-02 4.44e+03 3.28e+01 bond pdb=" O3' U B 46 " pdb=" P G B 47 " ideal model delta sigma weight residual 1.607 1.544 0.063 1.50e-02 4.44e+03 1.77e+01 bond pdb=" C PRO A1641 " pdb=" O PRO A1641 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.16e-02 7.43e+03 8.08e+00 bond pdb=" O3' C B 36 " pdb=" P C B 37 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.50e-02 4.44e+03 7.67e+00 ... (remaining 11399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 15538 3.84 - 7.67: 86 7.67 - 11.51: 8 11.51 - 15.35: 2 15.35 - 19.18: 4 Bond angle restraints: 15638 Sorted by residual: angle pdb=" O2' C B 36 " pdb=" C2' C B 36 " pdb=" C1' C B 36 " ideal model delta sigma weight residual 108.40 89.22 19.18 1.50e+00 4.44e-01 1.64e+02 angle pdb=" C4' U B 46 " pdb=" C3' U B 46 " pdb=" O3' U B 46 " ideal model delta sigma weight residual 109.40 91.58 17.82 1.50e+00 4.44e-01 1.41e+02 angle pdb=" C4' G B 47 " pdb=" C3' G B 47 " pdb=" O3' G B 47 " ideal model delta sigma weight residual 109.40 92.46 16.94 1.50e+00 4.44e-01 1.28e+02 angle pdb=" C4' C B 36 " pdb=" C3' C B 36 " pdb=" O3' C B 36 " ideal model delta sigma weight residual 113.00 128.95 -15.95 1.50e+00 4.44e-01 1.13e+02 angle pdb=" C4' A B 35 " pdb=" C3' A B 35 " pdb=" O3' A B 35 " ideal model delta sigma weight residual 109.40 95.53 13.87 1.50e+00 4.44e-01 8.55e+01 ... (remaining 15633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 6343 35.35 - 70.70: 328 70.70 - 106.05: 28 106.05 - 141.40: 1 141.40 - 176.75: 1 Dihedral angle restraints: 6701 sinusoidal: 3212 harmonic: 3489 Sorted by residual: dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 55.25 176.75 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASN A1449 " pdb=" C ASN A1449 " pdb=" N PRO A1450 " pdb=" CA PRO A1450 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ALA A 721 " pdb=" C ALA A 721 " pdb=" N VAL A 722 " pdb=" CA VAL A 722 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 6698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 1686 0.196 - 0.392: 18 0.392 - 0.588: 1 0.588 - 0.784: 0 0.784 - 0.980: 1 Chirality restraints: 1706 Sorted by residual: chirality pdb=" C2' A B 35 " pdb=" C3' A B 35 " pdb=" O2' A B 35 " pdb=" C1' A B 35 " both_signs ideal model delta sigma weight residual False -2.52 -1.54 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" C2' G B 47 " pdb=" C3' G B 47 " pdb=" O2' G B 47 " pdb=" C1' G B 47 " both_signs ideal model delta sigma weight residual False -2.52 -2.07 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C3' C B 36 " pdb=" C4' C B 36 " pdb=" O3' C B 36 " pdb=" C2' C B 36 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 1703 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 35 " 0.084 2.00e-02 2.50e+03 4.14e-02 4.70e+01 pdb=" N9 A B 35 " -0.105 2.00e-02 2.50e+03 pdb=" C8 A B 35 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A B 35 " 0.012 2.00e-02 2.50e+03 pdb=" C5 A B 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 35 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A B 35 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A B 35 " 0.010 2.00e-02 2.50e+03 pdb=" C2 A B 35 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A B 35 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A B 35 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " 0.049 2.00e-02 2.50e+03 2.33e-02 1.63e+01 pdb=" N9 G B 47 " -0.058 2.00e-02 2.50e+03 pdb=" C8 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G B 47 " 0.014 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G B 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G B 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G B 47 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 45 " 0.047 2.00e-02 2.50e+03 2.40e-02 1.29e+01 pdb=" N1 C B 45 " -0.050 2.00e-02 2.50e+03 pdb=" C2 C B 45 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C B 45 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C B 45 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B 45 " 0.020 2.00e-02 2.50e+03 pdb=" C5 C B 45 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C B 45 " -0.007 2.00e-02 2.50e+03 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 166 2.61 - 3.18: 8521 3.18 - 3.75: 20294 3.75 - 4.33: 28626 4.33 - 4.90: 44530 Nonbonded interactions: 102137 Sorted by model distance: nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 2.034 2.170 nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 2.044 2.170 nonbonded pdb=" O ILE A 940 " pdb=" OH TYR A1425 " model vdw 2.256 3.040 nonbonded pdb=" O GLU A1460 " pdb=" O2' C B 49 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A 922 " pdb=" OH TYR A1663 " model vdw 2.280 3.040 ... (remaining 102132 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 0.093 11420 Z= 0.262 Angle : 0.873 19.184 15659 Z= 0.490 Chirality : 0.060 0.980 1706 Planarity : 0.008 0.086 1814 Dihedral : 19.330 176.753 4467 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.91 % Allowed : 28.68 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.88 (0.21), residues: 1203 helix: -2.27 (0.20), residues: 341 sheet: -0.95 (0.35), residues: 196 loop : -0.66 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 193 TYR 0.019 0.002 TYR A 808 PHE 0.025 0.003 PHE A 805 TRP 0.053 0.003 TRP A1530 HIS 0.007 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.26 (11404) covalent geometry : angle 0.85846 / 0.49 (15638) hydrogen bonds : bond 0.23809 / 15.71 ( 383) hydrogen bonds : angle 9.19411 / 6.60 ( 1165) metal coordination : bond 0.00895 / 0.52 ( 16) metal coordination : angle 4.41734 / 2.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.416 Fit side-chains REVERT: A 7 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7120 (m-40) REVERT: A 68 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.7996 (pt) REVERT: A 168 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7928 (mtm-85) REVERT: A 368 LEU cc_start: 0.8077 (mt) cc_final: 0.7794 (mm) REVERT: A 773 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 781 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6965 (mp0) REVERT: A 918 LYS cc_start: 0.6782 (tppp) cc_final: 0.6331 (tptt) outliers start: 31 outliers final: 24 residues processed: 166 average time/residue: 0.5671 time to fit residues: 101.4784 Evaluate side-chains 158 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1502 GLN Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN A 919 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.150785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121931 restraints weight = 10539.275| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.48 r_work: 0.3251 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11420 Z= 0.145 Angle : 0.558 8.338 15659 Z= 0.296 Chirality : 0.043 0.316 1706 Planarity : 0.005 0.066 1814 Dihedral : 13.366 171.067 2019 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.03 % Allowed : 24.65 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.94 (0.22), residues: 1203 helix: -0.55 (0.25), residues: 355 sheet: -0.85 (0.36), residues: 189 loop : -0.48 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 168 TYR 0.010 0.001 TYR A1481 PHE 0.015 0.002 PHE A 659 TRP 0.016 0.001 TRP A 82 HIS 0.004 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (11404) covalent geometry : angle 0.55055 / 0.30 (15638) hydrogen bonds : bond 0.04958 / 3.24 ( 383) hydrogen bonds : angle 6.11170 / 4.45 ( 1165) metal coordination : bond 0.00465 / 0.27 ( 16) metal coordination : angle 2.50382 / 1.62 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.398 Fit side-chains REVERT: A 8 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8018 (pt) REVERT: A 13 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8267 (m) REVERT: A 95 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: A 123 LYS cc_start: 0.6794 (tttp) cc_final: 0.6398 (ttmm) REVERT: A 217 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7957 (tmtm) REVERT: A 238 GLU cc_start: 0.7353 (mp0) cc_final: 0.7024 (mm-30) REVERT: A 291 GLU cc_start: 0.7463 (pm20) cc_final: 0.7261 (pm20) REVERT: A 632 LYS cc_start: 0.6888 (tptt) cc_final: 0.6227 (tppp) REVERT: A 677 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: A 773 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: A 781 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7202 (mp0) REVERT: A 830 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.7673 (t80) REVERT: A 1502 GLN cc_start: 0.7794 (mt0) cc_final: 0.6251 (mm-40) REVERT: A 1617 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7529 (p90) REVERT: A 1671 ASN cc_start: 0.7307 (t0) cc_final: 0.7039 (t0) outliers start: 43 outliers final: 15 residues processed: 171 average time/residue: 0.6714 time to fit residues: 122.9066 Evaluate side-chains 160 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 0.0010 chunk 83 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.151101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122558 restraints weight = 10524.706| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.44 r_work: 0.3235 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11420 Z= 0.134 Angle : 0.524 8.228 15659 Z= 0.273 Chirality : 0.041 0.265 1706 Planarity : 0.004 0.055 1814 Dihedral : 13.086 169.545 1994 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.75 % Allowed : 25.12 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.40 (0.23), residues: 1203 helix: 0.43 (0.27), residues: 347 sheet: -0.87 (0.35), residues: 192 loop : -0.35 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1505 TYR 0.013 0.001 TYR A1595 PHE 0.015 0.001 PHE A1520 TRP 0.014 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (11404) covalent geometry : angle 0.51579 / 0.27 (15638) hydrogen bonds : bond 0.04220 / 2.77 ( 383) hydrogen bonds : angle 5.65999 / 4.12 ( 1165) metal coordination : bond 0.00471 / 0.30 ( 16) metal coordination : angle 2.55137 / 1.75 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.414 Fit side-chains REVERT: A 7 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: A 114 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: A 123 LYS cc_start: 0.7094 (tttp) cc_final: 0.6719 (ttmm) REVERT: A 217 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7983 (tmtm) REVERT: A 238 GLU cc_start: 0.7319 (mp0) cc_final: 0.7036 (mm-30) REVERT: A 290 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7578 (tp) REVERT: A 291 GLU cc_start: 0.7466 (pm20) cc_final: 0.7252 (pm20) REVERT: A 632 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6363 (tppp) REVERT: A 677 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 773 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7926 (mm-30) REVERT: A 781 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7270 (mp0) REVERT: A 830 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 1570 PHE cc_start: 0.7640 (p90) cc_final: 0.7261 (p90) REVERT: A 1600 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: A 1617 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.7528 (p90) REVERT: A 1671 ASN cc_start: 0.7326 (t0) cc_final: 0.7074 (t0) outliers start: 40 outliers final: 11 residues processed: 167 average time/residue: 0.7035 time to fit residues: 125.6925 Evaluate side-chains 156 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 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 = 0.3631 r_free = 0.3631 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117871 restraints weight = 10688.644| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.44 r_work: 0.3171 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11420 Z= 0.207 Angle : 0.574 8.584 15659 Z= 0.296 Chirality : 0.043 0.273 1706 Planarity : 0.005 0.060 1814 Dihedral : 13.083 165.032 1990 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.03 % Allowed : 24.37 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.29 (0.23), residues: 1203 helix: 0.57 (0.27), residues: 353 sheet: -0.86 (0.37), residues: 181 loop : -0.32 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 421 TYR 0.011 0.002 TYR A 702 PHE 0.019 0.002 PHE A 659 TRP 0.012 0.001 TRP A 82 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (11404) covalent geometry : angle 0.56535 / 0.30 (15638) hydrogen bonds : bond 0.04437 / 2.91 ( 383) hydrogen bonds : angle 5.68547 / 4.16 ( 1165) metal coordination : bond 0.00739 / 0.42 ( 16) metal coordination : angle 2.76357 / 1.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.315 Fit side-chains REVERT: A 7 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.6972 (m-40) REVERT: A 8 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8029 (pt) REVERT: A 114 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: A 123 LYS cc_start: 0.7246 (tttp) cc_final: 0.6872 (ttmm) REVERT: A 217 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7990 (tmtm) REVERT: A 290 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7677 (tp) REVERT: A 291 GLU cc_start: 0.7524 (pm20) cc_final: 0.7304 (pm20) REVERT: A 415 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: A 632 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6417 (tppp) REVERT: A 677 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 773 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: A 781 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7302 (mp0) REVERT: A 783 LEU cc_start: 0.8780 (tp) cc_final: 0.8579 (tm) REVERT: A 830 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8063 (t80) REVERT: A 1570 PHE cc_start: 0.7720 (p90) cc_final: 0.7307 (p90) REVERT: A 1600 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: A 1617 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7613 (p90) outliers start: 43 outliers final: 14 residues processed: 170 average time/residue: 0.7222 time to fit residues: 131.0942 Evaluate side-chains 167 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118966 restraints weight = 10213.257| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.33 r_work: 0.3135 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11420 Z= 0.203 Angle : 0.570 8.450 15659 Z= 0.295 Chirality : 0.043 0.273 1706 Planarity : 0.005 0.056 1814 Dihedral : 13.130 161.255 1990 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.31 % Allowed : 24.27 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.23), residues: 1203 helix: 0.71 (0.27), residues: 353 sheet: -0.92 (0.36), residues: 181 loop : -0.28 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1505 TYR 0.010 0.002 TYR A 702 PHE 0.018 0.002 PHE A 659 TRP 0.012 0.001 TRP A 82 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (11404) covalent geometry : angle 0.56115 / 0.29 (15638) hydrogen bonds : bond 0.04372 / 2.86 ( 383) hydrogen bonds : angle 5.68145 / 4.16 ( 1165) metal coordination : bond 0.00664 / 0.39 ( 16) metal coordination : angle 2.75071 / 1.89 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 0.415 Fit side-chains REVERT: A 7 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: A 73 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 114 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: A 123 LYS cc_start: 0.7338 (tttp) cc_final: 0.6934 (tttm) REVERT: A 217 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8186 (tttm) REVERT: A 290 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7734 (tp) REVERT: A 291 GLU cc_start: 0.7409 (pm20) cc_final: 0.7145 (pm20) REVERT: A 415 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: A 526 GLU cc_start: 0.7762 (mp0) cc_final: 0.7487 (mp0) REVERT: A 632 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6733 (tppp) REVERT: A 677 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 748 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5963 (tm-30) REVERT: A 773 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: A 781 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7306 (mp0) REVERT: A 830 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8208 (t80) REVERT: A 1529 GLU cc_start: 0.7816 (mm-30) cc_final: 0.6669 (pm20) REVERT: A 1600 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: A 1617 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7740 (p90) REVERT: A 1644 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7506 (ptm-80) outliers start: 46 outliers final: 15 residues processed: 180 average time/residue: 0.7398 time to fit residues: 142.1767 Evaluate side-chains 175 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1568 HIS A1649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.148518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120523 restraints weight = 10347.369| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.41 r_work: 0.3206 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11420 Z= 0.151 Angle : 0.539 8.488 15659 Z= 0.279 Chirality : 0.042 0.273 1706 Planarity : 0.004 0.053 1814 Dihedral : 13.125 161.887 1988 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.12 % Allowed : 25.12 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.08 (0.24), residues: 1203 helix: 0.93 (0.27), residues: 353 sheet: -0.95 (0.36), residues: 181 loop : -0.24 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1505 TYR 0.008 0.001 TYR A1481 PHE 0.017 0.002 PHE A 805 TRP 0.012 0.001 TRP A 82 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (11404) covalent geometry : angle 0.53135 / 0.28 (15638) hydrogen bonds : bond 0.03957 / 2.59 ( 383) hydrogen bonds : angle 5.55555 / 4.06 ( 1165) metal coordination : bond 0.00543 / 0.31 ( 16) metal coordination : angle 2.53261 / 1.70 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.423 Fit side-chains REVERT: A 7 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.6953 (m-40) REVERT: A 8 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8109 (pt) REVERT: A 69 LYS cc_start: 0.8348 (tttt) cc_final: 0.7960 (tttp) REVERT: A 73 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7338 (mt-10) REVERT: A 114 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: A 123 LYS cc_start: 0.7261 (tttp) cc_final: 0.6863 (tttm) REVERT: A 168 ARG cc_start: 0.8450 (mtm110) cc_final: 0.8134 (mtm-85) REVERT: A 217 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8060 (tttm) REVERT: A 290 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7736 (tp) REVERT: A 291 GLU cc_start: 0.7370 (pm20) cc_final: 0.7157 (pm20) REVERT: A 415 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: A 632 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6675 (tppp) REVERT: A 677 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 748 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.5810 (tm-30) REVERT: A 773 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: A 830 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 1570 PHE cc_start: 0.7826 (p90) cc_final: 0.7481 (p90) REVERT: A 1600 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: A 1617 HIS cc_start: 0.7985 (p-80) cc_final: 0.7700 (p90) REVERT: A 1644 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7431 (ptm-80) outliers start: 44 outliers final: 17 residues processed: 179 average time/residue: 0.7282 time to fit residues: 139.0715 Evaluate side-chains 170 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1644 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 119 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 34 optimal weight: 0.0040 chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.151497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.123853 restraints weight = 10276.866| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.40 r_work: 0.3239 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11420 Z= 0.127 Angle : 0.519 8.638 15659 Z= 0.269 Chirality : 0.041 0.271 1706 Planarity : 0.004 0.055 1814 Dihedral : 13.082 163.050 1986 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.50 % Allowed : 24.93 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1203 helix: 1.13 (0.28), residues: 351 sheet: -0.78 (0.36), residues: 181 loop : -0.20 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1505 TYR 0.008 0.001 TYR A1590 PHE 0.015 0.001 PHE A 805 TRP 0.011 0.001 TRP A1530 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11404) covalent geometry : angle 0.51197 / 0.27 (15638) hydrogen bonds : bond 0.03688 / 2.42 ( 383) hydrogen bonds : angle 5.42810 / 3.97 ( 1165) metal coordination : bond 0.00476 / 0.28 ( 16) metal coordination : angle 2.43271 / 1.60 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.483 Fit side-chains REVERT: A 7 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.6915 (m-40) REVERT: A 8 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8063 (pt) REVERT: A 69 LYS cc_start: 0.8323 (tttt) cc_final: 0.7952 (tttp) REVERT: A 73 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7275 (mt-10) REVERT: A 114 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: A 123 LYS cc_start: 0.7236 (tttp) cc_final: 0.6839 (tttm) REVERT: A 168 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8127 (mtm-85) REVERT: A 217 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8038 (tttm) REVERT: A 290 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7686 (tp) REVERT: A 291 GLU cc_start: 0.7397 (pm20) cc_final: 0.7157 (pm20) REVERT: A 372 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7536 (ttmm) REVERT: A 415 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: A 632 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6446 (tppp) REVERT: A 677 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: A 748 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5797 (tm-30) REVERT: A 773 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: A 781 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7321 (mp0) REVERT: A 830 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 1600 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: A 1617 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7646 (p90) outliers start: 48 outliers final: 19 residues processed: 178 average time/residue: 0.7246 time to fit residues: 137.7017 Evaluate side-chains 168 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118892 restraints weight = 10249.228| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.39 r_work: 0.3127 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11420 Z= 0.193 Angle : 0.566 9.222 15659 Z= 0.291 Chirality : 0.043 0.265 1706 Planarity : 0.005 0.079 1814 Dihedral : 13.097 160.499 1986 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.75 % Allowed : 25.49 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.02 (0.24), residues: 1203 helix: 1.00 (0.27), residues: 351 sheet: -0.95 (0.36), residues: 181 loop : -0.20 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1505 TYR 0.010 0.002 TYR A 702 PHE 0.016 0.002 PHE A 805 TRP 0.025 0.002 TRP A 82 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (11404) covalent geometry : angle 0.55809 / 0.29 (15638) hydrogen bonds : bond 0.04175 / 2.73 ( 383) hydrogen bonds : angle 5.54936 / 4.07 ( 1165) metal coordination : bond 0.00658 / 0.40 ( 16) metal coordination : angle 2.70530 / 1.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.501 Fit side-chains REVERT: A 7 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.6940 (m-40) REVERT: A 8 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8097 (pt) REVERT: A 73 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 114 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: A 123 LYS cc_start: 0.7230 (tttp) cc_final: 0.6820 (tttm) REVERT: A 159 ASP cc_start: 0.7292 (t70) cc_final: 0.7058 (t70) REVERT: A 168 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8226 (mtm-85) REVERT: A 217 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8095 (tttm) REVERT: A 290 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7913 (tp) REVERT: A 291 GLU cc_start: 0.7427 (pm20) cc_final: 0.7201 (pm20) REVERT: A 372 LYS cc_start: 0.7732 (mtpp) cc_final: 0.7524 (ttmm) REVERT: A 415 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: A 632 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6690 (tppp) REVERT: A 659 PHE cc_start: 0.6627 (t80) cc_final: 0.6174 (t80) REVERT: A 677 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: A 748 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.5864 (tm-30) REVERT: A 773 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: A 830 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 1446 ARG cc_start: 0.6823 (mmp80) cc_final: 0.6458 (mmp80) REVERT: A 1451 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6710 (mt-10) REVERT: A 1502 GLN cc_start: 0.7945 (mt0) cc_final: 0.6439 (mm-40) REVERT: A 1570 PHE cc_start: 0.7810 (p90) cc_final: 0.7423 (p90) REVERT: A 1600 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: A 1617 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7664 (p90) REVERT: A 1644 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7454 (ptm-80) outliers start: 40 outliers final: 17 residues processed: 169 average time/residue: 0.7220 time to fit residues: 130.3575 Evaluate side-chains 172 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1451 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122114 restraints weight = 10187.243| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.32 r_work: 0.3217 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11420 Z= 0.149 Angle : 0.541 9.314 15659 Z= 0.279 Chirality : 0.042 0.269 1706 Planarity : 0.005 0.076 1814 Dihedral : 13.097 160.956 1986 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.47 % Allowed : 25.68 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.24), residues: 1203 helix: 1.14 (0.28), residues: 351 sheet: -0.97 (0.36), residues: 181 loop : -0.18 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1505 TYR 0.008 0.001 TYR A1590 PHE 0.016 0.002 PHE A 805 TRP 0.020 0.001 TRP A1530 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (11404) covalent geometry : angle 0.53346 / 0.28 (15638) hydrogen bonds : bond 0.03856 / 2.52 ( 383) hydrogen bonds : angle 5.47068 / 4.01 ( 1165) metal coordination : bond 0.00529 / 0.31 ( 16) metal coordination : angle 2.54599 / 1.70 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.417 Fit side-chains REVERT: A 7 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.6950 (m-40) REVERT: A 8 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8132 (pt) REVERT: A 69 LYS cc_start: 0.8383 (tttt) cc_final: 0.8018 (tttp) REVERT: A 73 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7323 (mt-10) REVERT: A 114 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: A 123 LYS cc_start: 0.7294 (tttp) cc_final: 0.6895 (tttm) REVERT: A 159 ASP cc_start: 0.7288 (t70) cc_final: 0.7028 (t0) REVERT: A 217 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8115 (tttm) REVERT: A 290 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 291 GLU cc_start: 0.7451 (pm20) cc_final: 0.7229 (pm20) REVERT: A 372 LYS cc_start: 0.7772 (mtpp) cc_final: 0.7563 (ttmm) REVERT: A 415 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: A 632 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6757 (tppp) REVERT: A 659 PHE cc_start: 0.6539 (t80) cc_final: 0.6114 (t80) REVERT: A 677 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: A 748 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.5911 (tm-30) REVERT: A 773 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: A 830 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 1502 GLN cc_start: 0.8028 (mt0) cc_final: 0.6594 (mm-40) REVERT: A 1570 PHE cc_start: 0.7817 (p90) cc_final: 0.7445 (p90) REVERT: A 1600 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: A 1617 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7669 (p90) REVERT: A 1644 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7478 (ptm-80) REVERT: A 1669 LYS cc_start: 0.7115 (ttmt) cc_final: 0.6616 (mtmt) outliers start: 37 outliers final: 21 residues processed: 167 average time/residue: 0.6917 time to fit residues: 123.5919 Evaluate side-chains 176 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 0.0370 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.150510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122754 restraints weight = 10331.638| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.40 r_work: 0.3228 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11420 Z= 0.137 Angle : 0.537 9.534 15659 Z= 0.277 Chirality : 0.041 0.270 1706 Planarity : 0.005 0.070 1814 Dihedral : 13.054 161.669 1986 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.47 % Allowed : 25.77 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.12 (0.24), residues: 1203 helix: 1.20 (0.28), residues: 351 sheet: -0.91 (0.35), residues: 187 loop : -0.14 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 51 TYR 0.008 0.001 TYR A1590 PHE 0.015 0.001 PHE A 805 TRP 0.021 0.001 TRP A1530 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11404) covalent geometry : angle 0.52906 / 0.28 (15638) hydrogen bonds : bond 0.03729 / 2.44 ( 383) hydrogen bonds : angle 5.39633 / 3.96 ( 1165) metal coordination : bond 0.00495 / 0.29 ( 16) metal coordination : angle 2.50607 / 1.66 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.444 Fit side-chains REVERT: A 7 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.6909 (m-40) REVERT: A 8 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (pt) REVERT: A 69 LYS cc_start: 0.8330 (tttt) cc_final: 0.7959 (tttp) REVERT: A 73 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 114 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: A 123 LYS cc_start: 0.7244 (tttp) cc_final: 0.6836 (tttm) REVERT: A 159 ASP cc_start: 0.7251 (t70) cc_final: 0.6972 (t0) REVERT: A 290 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7805 (tp) REVERT: A 291 GLU cc_start: 0.7403 (pm20) cc_final: 0.7153 (pm20) REVERT: A 372 LYS cc_start: 0.7706 (mtpp) cc_final: 0.7480 (ttmm) REVERT: A 415 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: A 632 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6480 (tppp) REVERT: A 659 PHE cc_start: 0.6589 (t80) cc_final: 0.6107 (t80) REVERT: A 677 GLU cc_start: 0.7875 (tt0) cc_final: 0.7275 (mp0) REVERT: A 748 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.5771 (tm-30) REVERT: A 773 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: A 830 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7787 (t80) REVERT: A 1458 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8545 (m) REVERT: A 1600 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: A 1617 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7608 (p90) REVERT: A 1644 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7442 (ptm-80) REVERT: A 1669 LYS cc_start: 0.7044 (ttmt) cc_final: 0.6554 (mtmt) outliers start: 37 outliers final: 20 residues processed: 163 average time/residue: 0.7227 time to fit residues: 126.0631 Evaluate side-chains 169 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1584 GLN Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 0.0570 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 100 optimal weight: 0.0000 chunk 124 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 HIS A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.151732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124205 restraints weight = 10249.258| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.39 r_work: 0.3245 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11420 Z= 0.129 Angle : 0.529 9.613 15659 Z= 0.273 Chirality : 0.041 0.269 1706 Planarity : 0.005 0.071 1814 Dihedral : 12.948 162.487 1983 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.47 % Allowed : 25.68 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.24), residues: 1203 helix: 1.28 (0.28), residues: 351 sheet: -0.73 (0.35), residues: 180 loop : -0.11 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 51 TYR 0.008 0.001 TYR A 578 PHE 0.014 0.001 PHE A 805 TRP 0.025 0.001 TRP A1530 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11404) covalent geometry : angle 0.52178 / 0.27 (15638) hydrogen bonds : bond 0.03606 / 2.37 ( 383) hydrogen bonds : angle 5.33732 / 3.91 ( 1165) metal coordination : bond 0.00492 / 0.29 ( 16) metal coordination : angle 2.50740 / 1.64 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4247.58 seconds wall clock time: 73 minutes 27.49 seconds (4407.49 seconds total)