Starting phenix.real_space_refine on Tue Jul 29 12:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y81_33677/07_2025/7y81_33677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y81_33677/07_2025/7y81_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2025/7y81_33677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2025/7y81_33677.map" model { file = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2025/7y81_33677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y81_33677/07_2025/7y81_33677.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.280 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.98, per 1000 atoms: 0.63 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: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.47 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: 5.98 Time building geometry restraints manager: 3.26 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: 6439 35.35 - 70.70: 413 70.70 - 106.05: 43 106.05 - 141.40: 1 141.40 - 176.75: 1 Dihedral angle restraints: 6897 sinusoidal: 3408 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 6894 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.480 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 20.876 176.753 4663 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (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 TRP 0.053 0.003 TRP A1530 HIS 0.007 0.001 HIS A 924 PHE 0.025 0.003 PHE A 805 TYR 0.019 0.002 TYR A 808 ARG 0.023 0.001 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.23809 ( 383) hydrogen bonds : angle 9.19411 ( 1165) metal coordination : bond 0.00895 ( 16) metal coordination : angle 4.41734 ( 21) covalent geometry : bond 0.00551 (11404) covalent geometry : angle 0.85846 (15638) *********************** 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 : 1.099 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: 0.7657 (mm-30) cc_final: 0.7388 (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: 1.3529 time to fit residues: 241.7270 Evaluate side-chains 159 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3657 r_free = 0.3657 target = 0.148993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119783 restraints weight = 10470.463| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.48 r_work: 0.3180 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11420 Z= 0.171 Angle : 0.575 8.564 15659 Z= 0.305 Chirality : 0.043 0.305 1706 Planarity : 0.005 0.066 1814 Dihedral : 17.907 169.612 2215 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.84 % Allowed : 24.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1203 helix: -0.56 (0.24), residues: 354 sheet: -0.79 (0.36), residues: 191 loop : -0.45 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 82 HIS 0.004 0.001 HIS A 789 PHE 0.017 0.002 PHE A 659 TYR 0.011 0.001 TYR A1481 ARG 0.009 0.001 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 383) hydrogen bonds : angle 6.15256 ( 1165) metal coordination : bond 0.00509 ( 16) metal coordination : angle 2.57761 ( 21) covalent geometry : bond 0.00372 (11404) covalent geometry : angle 0.56807 (15638) *********************** 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 180 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 1.069 Fit side-chains REVERT: A 7 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.6925 (m-40) REVERT: A 13 THR cc_start: 0.8478 (t) cc_final: 0.8233 (m) REVERT: A 95 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6834 (m-30) REVERT: A 123 LYS cc_start: 0.6871 (tttp) cc_final: 0.6477 (ttmm) REVERT: A 215 HIS cc_start: 0.7817 (t-170) cc_final: 0.7541 (t-170) REVERT: A 217 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8074 (tmtm) REVERT: A 238 GLU cc_start: 0.7233 (mp0) cc_final: 0.6931 (mm-30) REVERT: A 290 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7515 (tp) REVERT: A 291 GLU cc_start: 0.7472 (pm20) cc_final: 0.7270 (pm20) REVERT: A 632 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6236 (tppp) REVERT: A 677 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: A 773 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: A 781 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7214 (mp0) REVERT: A 830 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 1502 GLN cc_start: 0.7828 (mt0) cc_final: 0.6286 (mm-40) REVERT: A 1617 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7581 (p90) outliers start: 41 outliers final: 13 residues processed: 170 average time/residue: 1.7405 time to fit residues: 315.2845 Evaluate side-chains 155 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 516 ASP 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 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 78 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 0.0980 chunk 79 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN A1671 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.150991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123651 restraints weight = 10687.624| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.40 r_work: 0.3200 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1405 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= 0.135 Angle : 0.525 7.724 15659 Z= 0.274 Chirality : 0.041 0.274 1706 Planarity : 0.004 0.056 1814 Dihedral : 17.808 168.575 2193 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.09 % Allowed : 25.96 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1203 helix: 0.35 (0.27), residues: 347 sheet: -0.87 (0.36), residues: 188 loop : -0.36 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 PHE 0.015 0.001 PHE A1520 TYR 0.008 0.001 TYR A 702 ARG 0.007 0.001 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 383) hydrogen bonds : angle 5.68643 ( 1165) metal coordination : bond 0.00493 ( 16) metal coordination : angle 2.55341 ( 21) covalent geometry : bond 0.00290 (11404) covalent geometry : angle 0.51655 (15638) *********************** 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 171 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.541 Fit side-chains REVERT: A 8 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8044 (pt) REVERT: A 114 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: A 123 LYS cc_start: 0.7167 (tttp) cc_final: 0.6795 (ttmm) REVERT: A 217 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8012 (tmtm) REVERT: A 238 GLU cc_start: 0.7364 (mp0) cc_final: 0.7094 (mm-30) REVERT: A 291 GLU cc_start: 0.7474 (pm20) cc_final: 0.7260 (pm20) REVERT: A 632 LYS cc_start: 0.7080 (tptt) cc_final: 0.6395 (tppp) REVERT: A 677 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: A 773 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 781 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7275 (mp0) REVERT: A 1570 PHE cc_start: 0.7656 (p90) cc_final: 0.7269 (p90) REVERT: A 1596 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: A 1600 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: A 1617 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7580 (p90) outliers start: 33 outliers final: 10 residues processed: 160 average time/residue: 2.2806 time to fit residues: 391.6557 Evaluate side-chains 151 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 206 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 464 LYS 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 806 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1458 VAL 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 1656 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 = 0.3687 r_free = 0.3687 target = 0.151096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123062 restraints weight = 10545.373| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.43 r_work: 0.3264 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1574 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= 0.138 Angle : 0.522 7.764 15659 Z= 0.271 Chirality : 0.041 0.276 1706 Planarity : 0.004 0.052 1814 Dihedral : 17.755 167.274 2186 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.94 % Allowed : 24.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1203 helix: 0.75 (0.27), residues: 347 sheet: -0.90 (0.36), residues: 188 loop : -0.28 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 PHE 0.014 0.001 PHE A 805 TYR 0.008 0.001 TYR A1481 ARG 0.008 0.000 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 383) hydrogen bonds : angle 5.51900 ( 1165) metal coordination : bond 0.00556 ( 16) metal coordination : angle 2.52552 ( 21) covalent geometry : bond 0.00301 (11404) covalent geometry : angle 0.51405 (15638) *********************** 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 188 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.357 Fit side-chains REVERT: A 8 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8030 (pt) REVERT: A 69 LYS cc_start: 0.8285 (tttt) cc_final: 0.7939 (tttp) REVERT: A 114 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: A 123 LYS cc_start: 0.7155 (tttp) cc_final: 0.6775 (ttmm) REVERT: A 217 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8004 (tmtm) REVERT: A 238 GLU cc_start: 0.7377 (mp0) cc_final: 0.7097 (mm-30) REVERT: A 290 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7650 (tp) REVERT: A 291 GLU cc_start: 0.7470 (pm20) cc_final: 0.7240 (pm20) REVERT: A 415 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: A 632 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6479 (tppp) REVERT: A 677 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 748 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5537 (tm-30) REVERT: A 773 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: A 781 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7362 (mp0) REVERT: A 830 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 1451 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7457 (mm-30) REVERT: A 1570 PHE cc_start: 0.7649 (p90) cc_final: 0.7254 (p90) REVERT: A 1600 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: A 1617 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7555 (p90) REVERT: A 1644 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7409 (ptm-80) outliers start: 42 outliers final: 11 residues processed: 175 average time/residue: 1.6425 time to fit residues: 307.2823 Evaluate side-chains 165 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1451 GLU 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 1618 VAL Chi-restraints excluded: chain A residue 1644 ARG 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 119 optimal weight: 0.0020 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 0.0010 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 92 optimal weight: 0.0980 overall best weight: 0.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 286 GLN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 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 = 0.3753 r_free = 0.3753 target = 0.156980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130706 restraints weight = 10487.687| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.37 r_work: 0.3335 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11420 Z= 0.100 Angle : 0.492 7.555 15659 Z= 0.256 Chirality : 0.040 0.274 1706 Planarity : 0.004 0.053 1814 Dihedral : 17.735 169.057 2186 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.91 % Allowed : 26.15 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1203 helix: 1.05 (0.28), residues: 350 sheet: -0.76 (0.36), residues: 178 loop : -0.27 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 82 HIS 0.003 0.000 HIS A 924 PHE 0.012 0.001 PHE A1520 TYR 0.007 0.001 TYR A 149 ARG 0.008 0.000 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 383) hydrogen bonds : angle 5.28320 ( 1165) metal coordination : bond 0.00405 ( 16) metal coordination : angle 2.39366 ( 21) covalent geometry : bond 0.00214 (11404) covalent geometry : angle 0.48487 (15638) *********************** 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 176 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.397 Fit side-chains REVERT: A 69 LYS cc_start: 0.8277 (tttt) cc_final: 0.7903 (tttp) REVERT: A 123 LYS cc_start: 0.7168 (tttp) cc_final: 0.6795 (ttmm) REVERT: A 168 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8018 (mtm-85) REVERT: A 238 GLU cc_start: 0.7240 (mp0) cc_final: 0.7013 (mm-30) REVERT: A 290 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7627 (tp) REVERT: A 415 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: A 511 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.8086 (mtt90) REVERT: A 632 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6465 (tppp) REVERT: A 677 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: A 748 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5476 (tm-30) REVERT: A 773 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: A 781 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7273 (mp0) REVERT: A 830 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7374 (t80) REVERT: A 1570 PHE cc_start: 0.7489 (p90) cc_final: 0.7136 (p90) REVERT: A 1600 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: A 1617 HIS cc_start: 0.7651 (p-80) cc_final: 0.7377 (p90) outliers start: 31 outliers final: 7 residues processed: 168 average time/residue: 2.0311 time to fit residues: 367.3433 Evaluate side-chains 147 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 415 GLU 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 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1600 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.0570 chunk 34 optimal weight: 0.0030 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.153918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126263 restraints weight = 10584.389| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.43 r_work: 0.3291 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1782 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= 0.122 Angle : 0.508 8.404 15659 Z= 0.262 Chirality : 0.041 0.268 1706 Planarity : 0.004 0.052 1814 Dihedral : 17.711 168.072 2181 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.37 % Allowed : 25.59 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1203 helix: 1.23 (0.28), residues: 352 sheet: -0.76 (0.35), residues: 185 loop : -0.19 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 82 HIS 0.003 0.001 HIS A 924 PHE 0.013 0.001 PHE A1520 TYR 0.007 0.001 TYR A1481 ARG 0.008 0.000 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 383) hydrogen bonds : angle 5.22563 ( 1165) metal coordination : bond 0.00483 ( 16) metal coordination : angle 2.43522 ( 21) covalent geometry : bond 0.00267 (11404) covalent geometry : angle 0.50038 (15638) *********************** 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 178 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.135 Fit side-chains REVERT: A 69 LYS cc_start: 0.8264 (tttt) cc_final: 0.7918 (tttp) REVERT: A 114 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: A 123 LYS cc_start: 0.7138 (tttp) cc_final: 0.6762 (ttmm) REVERT: A 168 ARG cc_start: 0.8376 (mtm110) cc_final: 0.8090 (mtm-85) REVERT: A 217 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7919 (tmtm) REVERT: A 238 GLU cc_start: 0.7339 (mp0) cc_final: 0.7077 (mm-30) REVERT: A 290 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7764 (tp) REVERT: A 415 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: A 632 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6391 (tppp) REVERT: A 677 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: A 748 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5502 (tm-30) REVERT: A 773 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7795 (mm-30) REVERT: A 781 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7247 (mp0) REVERT: A 830 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7403 (t80) REVERT: A 1570 PHE cc_start: 0.7519 (p90) cc_final: 0.7140 (p90) REVERT: A 1600 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: A 1617 HIS cc_start: 0.7636 (p-80) cc_final: 0.7370 (p90) REVERT: A 1644 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7385 (ptm-80) REVERT: A 1669 LYS cc_start: 0.7232 (ttmt) cc_final: 0.6512 (mtmt) outliers start: 36 outliers final: 11 residues processed: 168 average time/residue: 1.4809 time to fit residues: 265.6748 Evaluate side-chains 156 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 493 VAL Chi-restraints excluded: chain A residue 513 THR 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 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1644 ARG Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124015 restraints weight = 10523.166| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.42 r_work: 0.3258 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1802 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= 0.153 Angle : 0.530 9.021 15659 Z= 0.273 Chirality : 0.041 0.266 1706 Planarity : 0.004 0.050 1814 Dihedral : 17.707 165.866 2181 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.81 % Allowed : 25.96 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1203 helix: 1.21 (0.27), residues: 351 sheet: -0.69 (0.36), residues: 185 loop : -0.14 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 82 HIS 0.004 0.001 HIS A 727 PHE 0.014 0.002 PHE A1520 TYR 0.008 0.001 TYR A1481 ARG 0.008 0.000 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 383) hydrogen bonds : angle 5.30223 ( 1165) metal coordination : bond 0.00552 ( 16) metal coordination : angle 2.56445 ( 21) covalent geometry : bond 0.00338 (11404) covalent geometry : angle 0.52196 (15638) *********************** 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 172 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.250 Fit side-chains REVERT: A 69 LYS cc_start: 0.8292 (tttt) cc_final: 0.7874 (tttp) REVERT: A 73 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 114 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: A 123 LYS cc_start: 0.7254 (tttp) cc_final: 0.6884 (ttmm) REVERT: A 168 ARG cc_start: 0.8404 (mtm110) cc_final: 0.8126 (mtm-85) REVERT: A 217 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7959 (tmtm) REVERT: A 238 GLU cc_start: 0.7429 (mp0) cc_final: 0.7164 (mm-30) REVERT: A 290 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7743 (tp) REVERT: A 415 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: A 632 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6399 (tppp) REVERT: A 659 PHE cc_start: 0.6444 (t80) cc_final: 0.5966 (t80) REVERT: A 677 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 748 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5613 (tm-30) REVERT: A 773 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: A 830 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7628 (t80) REVERT: A 1570 PHE cc_start: 0.7604 (p90) cc_final: 0.7218 (p90) REVERT: A 1600 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: A 1617 HIS cc_start: 0.7722 (p-80) cc_final: 0.7467 (p90) REVERT: A 1644 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7422 (ptm-80) REVERT: A 1669 LYS cc_start: 0.7243 (ttmt) cc_final: 0.6520 (mtmt) outliers start: 30 outliers final: 14 residues processed: 163 average time/residue: 1.5209 time to fit residues: 264.8573 Evaluate side-chains 163 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 493 VAL Chi-restraints excluded: chain A residue 513 THR 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 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 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 Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.0570 chunk 60 optimal weight: 2.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115698 restraints weight = 10311.000| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.41 r_work: 0.3092 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11420 Z= 0.264 Angle : 0.630 9.416 15659 Z= 0.325 Chirality : 0.045 0.264 1706 Planarity : 0.005 0.048 1814 Dihedral : 17.753 157.671 2181 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.03 % Allowed : 24.93 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1203 helix: 0.75 (0.27), residues: 353 sheet: -1.03 (0.36), residues: 185 loop : -0.20 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 82 HIS 0.005 0.001 HIS A 727 PHE 0.022 0.002 PHE A 659 TYR 0.013 0.002 TYR A 661 ARG 0.008 0.001 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 383) hydrogen bonds : angle 5.68767 ( 1165) metal coordination : bond 0.00912 ( 16) metal coordination : angle 2.98661 ( 21) covalent geometry : bond 0.00583 (11404) covalent geometry : angle 0.62069 (15638) *********************** 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 192 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 1.145 Fit side-chains REVERT: A 73 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7105 (mt-10) REVERT: A 114 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: A 123 LYS cc_start: 0.7258 (tttp) cc_final: 0.6843 (tttm) REVERT: A 159 ASP cc_start: 0.7298 (t70) cc_final: 0.7014 (t70) REVERT: A 217 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8118 (tttm) REVERT: A 344 LYS cc_start: 0.7723 (mtpp) cc_final: 0.7261 (tttt) REVERT: A 372 LYS cc_start: 0.7717 (mttp) cc_final: 0.7496 (ttmm) REVERT: A 415 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: A 632 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6632 (tppp) REVERT: A 659 PHE cc_start: 0.6684 (t80) cc_final: 0.6208 (t80) REVERT: A 677 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: A 748 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: A 773 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8046 (mm-30) REVERT: A 1502 GLN cc_start: 0.7924 (mt0) cc_final: 0.6402 (mm-40) REVERT: A 1600 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: A 1617 HIS cc_start: 0.8014 (p-80) cc_final: 0.7764 (p90) REVERT: A 1644 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7486 (ptm-80) outliers start: 43 outliers final: 15 residues processed: 180 average time/residue: 1.6742 time to fit residues: 322.6176 Evaluate side-chains 168 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 513 THR 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 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 858 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.149221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121257 restraints weight = 10378.364| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.40 r_work: 0.3222 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2048 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= 0.152 Angle : 0.549 9.160 15659 Z= 0.284 Chirality : 0.042 0.275 1706 Planarity : 0.004 0.049 1814 Dihedral : 17.718 160.083 2181 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.72 % Allowed : 26.24 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1203 helix: 1.05 (0.27), residues: 353 sheet: -1.05 (0.35), residues: 185 loop : -0.16 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 82 HIS 0.003 0.001 HIS A 727 PHE 0.018 0.002 PHE A 805 TYR 0.009 0.001 TYR A1595 ARG 0.011 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 383) hydrogen bonds : angle 5.46778 ( 1165) metal coordination : bond 0.00555 ( 16) metal coordination : angle 2.49443 ( 21) covalent geometry : bond 0.00333 (11404) covalent geometry : angle 0.54154 (15638) *********************** 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 178 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8335 (tttt) cc_final: 0.7957 (tttp) REVERT: A 73 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 114 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: A 123 LYS cc_start: 0.7240 (tttp) cc_final: 0.6829 (tttm) REVERT: A 159 ASP cc_start: 0.7255 (t70) cc_final: 0.7005 (t0) REVERT: A 168 ARG cc_start: 0.8424 (mtm110) cc_final: 0.8052 (mtm-85) REVERT: A 217 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8132 (tttm) REVERT: A 344 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7146 (tttt) REVERT: A 372 LYS cc_start: 0.7710 (mttp) cc_final: 0.7487 (ttmm) REVERT: A 415 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: A 632 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6714 (tppp) REVERT: A 659 PHE cc_start: 0.6529 (t80) cc_final: 0.6085 (t80) REVERT: A 677 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: A 748 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.5847 (tm-30) REVERT: A 773 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: A 830 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8129 (t80) REVERT: A 1529 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6462 (pm20) REVERT: A 1570 PHE cc_start: 0.7806 (p90) cc_final: 0.7468 (p90) REVERT: A 1600 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: A 1617 HIS cc_start: 0.7921 (p-80) cc_final: 0.7641 (p90) REVERT: A 1644 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7431 (ptm-80) outliers start: 29 outliers final: 13 residues processed: 170 average time/residue: 1.5842 time to fit residues: 289.3348 Evaluate side-chains 167 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 217 LYS 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 513 THR 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 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1529 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 75 optimal weight: 0.0170 chunk 52 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125495 restraints weight = 10324.825| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.40 r_work: 0.3261 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2054 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= 0.124 Angle : 0.527 9.181 15659 Z= 0.272 Chirality : 0.041 0.272 1706 Planarity : 0.004 0.056 1814 Dihedral : 17.676 163.056 2181 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.16 % Allowed : 26.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1203 helix: 1.41 (0.28), residues: 345 sheet: -0.84 (0.34), residues: 188 loop : -0.06 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 82 HIS 0.003 0.001 HIS A 924 PHE 0.016 0.001 PHE A 805 TYR 0.007 0.001 TYR A 850 ARG 0.012 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 383) hydrogen bonds : angle 5.26564 ( 1165) metal coordination : bond 0.00481 ( 16) metal coordination : angle 2.39326 ( 21) covalent geometry : bond 0.00274 (11404) covalent geometry : angle 0.51963 (15638) ********************** 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 166 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7065 (mt-10) REVERT: A 114 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: A 123 LYS cc_start: 0.6990 (tttp) cc_final: 0.6576 (tttm) REVERT: A 159 ASP cc_start: 0.7209 (t70) cc_final: 0.6941 (t0) REVERT: A 168 ARG cc_start: 0.8377 (mtm110) cc_final: 0.8081 (mtm-85) REVERT: A 214 GLU cc_start: 0.7459 (tp30) cc_final: 0.7051 (tp30) REVERT: A 217 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8129 (tttm) REVERT: A 238 GLU cc_start: 0.7147 (mp0) cc_final: 0.6884 (mm-30) REVERT: A 372 LYS cc_start: 0.7693 (mttp) cc_final: 0.7461 (ttmm) REVERT: A 415 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 511 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.8205 (mtt90) REVERT: A 632 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6694 (tppp) REVERT: A 659 PHE cc_start: 0.6545 (t80) cc_final: 0.6082 (t80) REVERT: A 677 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 689 SER cc_start: 0.8248 (m) cc_final: 0.8007 (t) REVERT: A 748 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5743 (tm-30) REVERT: A 773 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: A 1458 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8510 (m) REVERT: A 1529 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6466 (pm20) REVERT: A 1600 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7822 (pt0) REVERT: A 1617 HIS cc_start: 0.7802 (p-80) cc_final: 0.7528 (p90) REVERT: A 1644 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7428 (ptm-80) REVERT: A 1669 LYS cc_start: 0.7065 (ttmt) cc_final: 0.6533 (mtmt) outliers start: 23 outliers final: 11 residues processed: 158 average time/residue: 2.2081 time to fit residues: 373.9223 Evaluate side-chains 161 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 217 LYS 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 513 THR 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 677 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1529 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 0.0070 chunk 46 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 0.0000 chunk 30 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 HIS ** A1547 HIS ** 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 = 0.3729 r_free = 0.3729 target = 0.154932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127553 restraints weight = 10417.383| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.41 r_work: 0.3301 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11420 Z= 0.113 Angle : 0.518 9.289 15659 Z= 0.267 Chirality : 0.040 0.269 1706 Planarity : 0.004 0.057 1814 Dihedral : 17.616 165.005 2181 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.25 % Allowed : 26.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1203 helix: 1.40 (0.28), residues: 352 sheet: -0.75 (0.34), residues: 184 loop : -0.05 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1530 HIS 0.003 0.001 HIS A 924 PHE 0.014 0.001 PHE A 805 TYR 0.007 0.001 TYR A 578 ARG 0.013 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 383) hydrogen bonds : angle 5.14193 ( 1165) metal coordination : bond 0.00459 ( 16) metal coordination : angle 2.37301 ( 21) covalent geometry : bond 0.00249 (11404) covalent geometry : angle 0.51058 (15638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10389.21 seconds wall clock time: 193 minutes 44.81 seconds (11624.81 seconds total)