Starting phenix.real_space_refine on Wed May 14 04:16:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y81_33677/05_2025/7y81_33677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y81_33677/05_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_33677/05_2025/7y81_33677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y81_33677/05_2025/7y81_33677.map" model { file = "/net/cci-nas-00/data/ceres_data/7y81_33677/05_2025/7y81_33677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y81_33677/05_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-5687/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: 6.48, per 1000 atoms: 0.59 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 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: 4.30 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: 6.25 Time building geometry restraints manager: 2.95 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: 0.860 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.280 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.780 ------------------------------------------------------------------------------- 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 : 1.062 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: 1.2774 time to fit residues: 228.7558 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 : 1.188 ------------------------------------------------------------------------------- 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 = 0.148994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119774 restraints weight = 10470.262| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.48 r_work: 0.3173 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1106 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 8.559 15659 Z= 0.305 Chirality : 0.043 0.305 1706 Planarity : 0.005 0.066 1814 Dihedral : 17.907 169.609 2215 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.63 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 0.05007 ( 383) hydrogen bonds : angle 6.15223 ( 1165) metal coordination : bond 0.00509 ( 16) metal coordination : angle 2.57801 ( 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 : 1.164 Fit side-chains REVERT: A 7 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6916 (m-40) REVERT: A 13 THR cc_start: 0.8480 (t) cc_final: 0.8235 (m) REVERT: A 95 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: A 123 LYS cc_start: 0.6877 (tttp) cc_final: 0.6482 (ttmm) REVERT: A 215 HIS cc_start: 0.7817 (t-170) cc_final: 0.7544 (t-170) REVERT: A 217 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8086 (tmtm) REVERT: A 238 GLU cc_start: 0.7243 (mp0) cc_final: 0.6940 (mm-30) REVERT: A 290 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7520 (tp) REVERT: A 291 GLU cc_start: 0.7471 (pm20) cc_final: 0.7268 (pm20) REVERT: A 632 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6243 (tppp) REVERT: A 677 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: A 773 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: A 781 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7214 (mp0) REVERT: A 830 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.7924 (t80) REVERT: A 1502 GLN cc_start: 0.7831 (mt0) cc_final: 0.6287 (mm-40) REVERT: A 1617 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7589 (p90) outliers start: 41 outliers final: 13 residues processed: 170 average time/residue: 1.4922 time to fit residues: 271.3739 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 : 1.056 ------------------------------------------------------------------------------- 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: 0.2980 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 0.0000 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 85 optimal weight: 0.0060 chunk 80 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.154812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128249 restraints weight = 10662.061| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.38 r_work: 0.3319 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11420 Z= 0.114 Angle : 0.508 7.457 15659 Z= 0.266 Chirality : 0.041 0.274 1706 Planarity : 0.004 0.056 1814 Dihedral : 17.807 170.092 2193 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.56 % Allowed : 25.59 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.23), residues: 1203 helix: 0.42 (0.27), residues: 348 sheet: -0.78 (0.36), residues: 182 loop : -0.39 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 PHE 0.014 0.001 PHE A1520 TYR 0.007 0.001 TYR A 149 ARG 0.008 0.001 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 383) hydrogen bonds : angle 5.60163 ( 1165) metal coordination : bond 0.00638 ( 16) metal coordination : angle 2.46412 ( 21) covalent geometry : bond 0.00242 (11404) covalent geometry : angle 0.50072 (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 181 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 1.078 Fit side-chains REVERT: A 8 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8007 (pt) REVERT: A 69 LYS cc_start: 0.8294 (tttt) cc_final: 0.7945 (tttp) REVERT: A 114 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: A 123 LYS cc_start: 0.7166 (tttp) cc_final: 0.6796 (ttmm) REVERT: A 217 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7956 (tmtm) REVERT: A 238 GLU cc_start: 0.7269 (mp0) cc_final: 0.7018 (mm-30) REVERT: A 291 GLU cc_start: 0.7452 (pm20) cc_final: 0.7237 (pm20) REVERT: A 632 LYS cc_start: 0.7000 (tptt) cc_final: 0.6336 (tppp) REVERT: A 677 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: A 773 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 781 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7291 (mp0) REVERT: A 1570 PHE cc_start: 0.7620 (p90) cc_final: 0.7249 (p90) REVERT: A 1600 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: A 1617 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7527 (p90) outliers start: 38 outliers final: 10 residues processed: 167 average time/residue: 1.4566 time to fit residues: 260.4307 Evaluate side-chains 154 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 516 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 657 CYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 112 optimal weight: 0.0170 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1568 HIS A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.125348 restraints weight = 10618.142| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.39 r_work: 0.3280 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1583 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= 0.127 Angle : 0.514 7.626 15659 Z= 0.266 Chirality : 0.041 0.269 1706 Planarity : 0.004 0.051 1814 Dihedral : 17.756 168.870 2186 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.66 % Allowed : 24.93 % 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: -0.16 (0.23), residues: 1203 helix: 0.77 (0.27), residues: 350 sheet: -0.76 (0.37), residues: 179 loop : -0.31 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 82 HIS 0.003 0.001 HIS A 924 PHE 0.013 0.001 PHE A1520 TYR 0.008 0.001 TYR A1481 ARG 0.008 0.000 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 383) hydrogen bonds : angle 5.42818 ( 1165) metal coordination : bond 0.00557 ( 16) metal coordination : angle 2.48534 ( 21) covalent geometry : bond 0.00276 (11404) covalent geometry : angle 0.50616 (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 181 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 1.132 Fit side-chains REVERT: A 8 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8018 (pt) REVERT: A 69 LYS cc_start: 0.8300 (tttt) cc_final: 0.7933 (tttp) REVERT: A 123 LYS cc_start: 0.7138 (tttp) cc_final: 0.6760 (ttmm) REVERT: A 168 ARG cc_start: 0.8398 (mtm110) cc_final: 0.8143 (mtm-85) REVERT: A 217 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7954 (tmtm) REVERT: A 238 GLU cc_start: 0.7343 (mp0) cc_final: 0.7083 (mm-30) REVERT: A 290 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7603 (tp) REVERT: A 291 GLU cc_start: 0.7469 (pm20) cc_final: 0.7246 (pm20) REVERT: A 415 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: A 632 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6461 (tppp) REVERT: A 677 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 773 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: A 781 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7274 (mp0) REVERT: A 830 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7584 (t80) REVERT: A 1570 PHE cc_start: 0.7581 (p90) cc_final: 0.7207 (p90) REVERT: A 1600 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: A 1617 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7490 (p90) REVERT: A 1644 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7399 (ptm-80) outliers start: 39 outliers final: 9 residues processed: 168 average time/residue: 1.4323 time to fit residues: 257.8042 Evaluate side-chains 158 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 415 GLU 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 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** 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 = 0.3685 r_free = 0.3685 target = 0.150668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122391 restraints weight = 10388.256| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.42 r_work: 0.3159 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11420 Z= 0.169 Angle : 0.541 7.805 15659 Z= 0.280 Chirality : 0.042 0.264 1706 Planarity : 0.004 0.049 1814 Dihedral : 17.747 165.251 2184 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.75 % Allowed : 24.65 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.23), residues: 1203 helix: 0.93 (0.27), residues: 351 sheet: -0.82 (0.36), residues: 187 loop : -0.23 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 82 HIS 0.004 0.001 HIS A 727 PHE 0.016 0.002 PHE A1520 TYR 0.009 0.001 TYR A 702 ARG 0.010 0.001 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 383) hydrogen bonds : angle 5.47225 ( 1165) metal coordination : bond 0.00616 ( 16) metal coordination : angle 2.62047 ( 21) covalent geometry : bond 0.00372 (11404) covalent geometry : angle 0.53269 (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 186 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.092 Fit side-chains REVERT: A 8 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8041 (pt) REVERT: A 73 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7130 (mt-10) REVERT: A 114 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: A 123 LYS cc_start: 0.7281 (tttp) cc_final: 0.6912 (ttmm) REVERT: A 217 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8047 (tmtm) REVERT: A 290 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 415 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: A 632 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6601 (tppp) REVERT: A 677 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: A 748 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5709 (tm-30) REVERT: A 773 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: A 781 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7364 (mp0) REVERT: A 830 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.7818 (t80) REVERT: A 1600 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: A 1617 HIS cc_start: 0.7885 (p-80) cc_final: 0.7618 (p90) REVERT: A 1644 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7443 (ptm-80) outliers start: 40 outliers final: 12 residues processed: 172 average time/residue: 1.4305 time to fit residues: 263.7826 Evaluate side-chains 163 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 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 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.150163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122001 restraints weight = 10500.745| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.42 r_work: 0.3147 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1789 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= 0.164 Angle : 0.539 8.146 15659 Z= 0.279 Chirality : 0.042 0.268 1706 Planarity : 0.004 0.051 1814 Dihedral : 17.745 163.221 2182 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.28 % Allowed : 25.12 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.27), residues: 351 sheet: -0.80 (0.36), residues: 187 loop : -0.21 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 82 HIS 0.004 0.001 HIS A 727 PHE 0.014 0.002 PHE A 805 TYR 0.009 0.001 TYR A1481 ARG 0.009 0.001 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 383) hydrogen bonds : angle 5.46143 ( 1165) metal coordination : bond 0.00576 ( 16) metal coordination : angle 2.57048 ( 21) covalent geometry : bond 0.00360 (11404) covalent geometry : angle 0.53116 (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 177 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.237 Fit side-chains REVERT: A 8 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8092 (pt) REVERT: A 73 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 114 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: A 123 LYS cc_start: 0.7280 (tttp) cc_final: 0.6884 (tttm) REVERT: A 168 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8187 (mtm-85) REVERT: A 217 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8078 (tttm) REVERT: A 290 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7812 (tp) REVERT: A 415 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: A 632 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6647 (tppp) REVERT: A 677 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 748 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5763 (tm-30) REVERT: A 773 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: A 781 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7327 (mp0) REVERT: A 830 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 1529 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6243 (pm20) REVERT: A 1570 PHE cc_start: 0.7800 (p90) cc_final: 0.7445 (p90) REVERT: A 1600 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: A 1617 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7662 (p90) REVERT: A 1644 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7458 (ptm-80) outliers start: 35 outliers final: 14 residues processed: 167 average time/residue: 1.5098 time to fit residues: 269.2581 Evaluate side-chains 166 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 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 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 954 ILE 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 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=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: 8.9990 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 215 HIS A 286 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116325 restraints weight = 10369.576| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.41 r_work: 0.3141 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11420 Z= 0.248 Angle : 0.609 8.763 15659 Z= 0.313 Chirality : 0.045 0.264 1706 Planarity : 0.005 0.051 1814 Dihedral : 17.767 158.747 2182 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.31 % Allowed : 24.46 % 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: -0.20 (0.23), residues: 1203 helix: 0.73 (0.27), residues: 353 sheet: -0.98 (0.36), residues: 183 loop : -0.27 (0.24), residues: 667 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 0.020 0.002 PHE A 659 TYR 0.012 0.002 TYR A 702 ARG 0.010 0.001 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 383) hydrogen bonds : angle 5.67027 ( 1165) metal coordination : bond 0.00845 ( 16) metal coordination : angle 2.97110 ( 21) covalent geometry : bond 0.00552 (11404) covalent geometry : angle 0.59946 (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 190 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.6984 (m-40) REVERT: A 73 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 114 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: A 123 LYS cc_start: 0.7266 (tttp) cc_final: 0.6854 (tttm) REVERT: A 159 ASP cc_start: 0.7343 (t70) cc_final: 0.7101 (t70) REVERT: A 168 ARG cc_start: 0.8459 (mtm110) cc_final: 0.8220 (mtm-85) REVERT: A 217 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8145 (tttm) REVERT: A 290 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 415 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: A 632 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6738 (tppp) REVERT: A 659 PHE cc_start: 0.6630 (t80) cc_final: 0.6167 (t80) REVERT: A 677 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 748 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5914 (tm-30) REVERT: A 773 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: A 1502 GLN cc_start: 0.7982 (mt0) cc_final: 0.6439 (mm-40) REVERT: A 1529 GLU cc_start: 0.7917 (mm-30) cc_final: 0.6637 (pm20) REVERT: A 1570 PHE cc_start: 0.7814 (p90) cc_final: 0.7470 (p90) REVERT: A 1600 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: A 1617 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7795 (p90) REVERT: A 1644 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7433 (ptm-80) outliers start: 46 outliers final: 17 residues processed: 175 average time/residue: 1.4578 time to fit residues: 274.1582 Evaluate side-chains 171 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 531 ILE 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 855 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.147096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118974 restraints weight = 10287.352| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.40 r_work: 0.3129 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11420 Z= 0.175 Angle : 0.563 8.684 15659 Z= 0.290 Chirality : 0.042 0.270 1706 Planarity : 0.005 0.055 1814 Dihedral : 17.755 159.491 2182 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.47 % Allowed : 25.68 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.24), residues: 1203 helix: 0.92 (0.27), residues: 353 sheet: -0.96 (0.36), residues: 181 loop : -0.23 (0.24), residues: 669 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 A1481 ARG 0.012 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 383) hydrogen bonds : angle 5.57649 ( 1165) metal coordination : bond 0.00619 ( 16) metal coordination : angle 2.66669 ( 21) covalent geometry : bond 0.00387 (11404) covalent geometry : angle 0.55472 (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 182 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.210 Fit side-chains REVERT: A 7 ASN cc_start: 0.7574 (m-40) cc_final: 0.6993 (m-40) REVERT: A 8 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8137 (pt) REVERT: A 73 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7192 (mt-10) REVERT: A 114 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: A 123 LYS cc_start: 0.7249 (tttp) cc_final: 0.6839 (tttm) REVERT: A 159 ASP cc_start: 0.7291 (t70) cc_final: 0.7040 (t70) REVERT: A 168 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8231 (mtm-85) REVERT: A 217 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8095 (tttm) REVERT: A 290 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7993 (tp) REVERT: A 415 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: A 632 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6684 (tppp) REVERT: A 659 PHE cc_start: 0.6565 (t80) cc_final: 0.6136 (t80) REVERT: A 677 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: A 748 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5911 (tm-30) REVERT: A 773 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: A 830 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8270 (t80) REVERT: A 1502 GLN cc_start: 0.7942 (mt0) cc_final: 0.6433 (mm-40) REVERT: A 1570 PHE cc_start: 0.7799 (p90) cc_final: 0.7454 (p90) REVERT: A 1600 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: A 1617 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7772 (p90) outliers start: 37 outliers final: 15 residues processed: 171 average time/residue: 1.4018 time to fit residues: 256.0559 Evaluate side-chains 166 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 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 948 GLU Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.146257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117953 restraints weight = 10365.239| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.41 r_work: 0.3115 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11420 Z= 0.199 Angle : 0.580 8.942 15659 Z= 0.298 Chirality : 0.043 0.267 1706 Planarity : 0.005 0.095 1814 Dihedral : 17.746 159.061 2182 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.47 % Allowed : 25.96 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.24), residues: 1203 helix: 0.89 (0.27), residues: 351 sheet: -1.01 (0.35), residues: 183 loop : -0.22 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 82 HIS 0.003 0.001 HIS A 727 PHE 0.018 0.002 PHE A 805 TYR 0.011 0.002 TYR A1590 ARG 0.013 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 383) hydrogen bonds : angle 5.59725 ( 1165) metal coordination : bond 0.00668 ( 16) metal coordination : angle 2.75236 ( 21) covalent geometry : bond 0.00443 (11404) covalent geometry : angle 0.57130 (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 176 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.075 Fit side-chains REVERT: A 7 ASN cc_start: 0.7510 (m-40) cc_final: 0.6929 (m-40) REVERT: A 8 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8148 (pt) REVERT: A 73 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 114 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: A 123 LYS cc_start: 0.7264 (tttp) cc_final: 0.6858 (tttm) REVERT: A 159 ASP cc_start: 0.7307 (t70) cc_final: 0.7044 (t70) REVERT: A 168 ARG cc_start: 0.8451 (mtm110) cc_final: 0.8232 (mtm-85) REVERT: A 217 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8081 (tttm) REVERT: A 290 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8007 (tp) REVERT: A 415 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: A 454 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6244 (pt0) REVERT: A 632 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6715 (tppp) REVERT: A 659 PHE cc_start: 0.6636 (t80) cc_final: 0.6174 (t80) REVERT: A 677 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 748 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5897 (tm-30) REVERT: A 773 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: A 830 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8221 (t80) REVERT: A 1451 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6624 (mt-10) REVERT: A 1502 GLN cc_start: 0.7938 (mt0) cc_final: 0.6431 (mm-40) REVERT: A 1570 PHE cc_start: 0.7809 (p90) cc_final: 0.7455 (p90) REVERT: A 1600 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: A 1617 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7786 (p90) REVERT: A 1644 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7437 (ptm-80) outliers start: 37 outliers final: 18 residues processed: 164 average time/residue: 1.4615 time to fit residues: 256.0310 Evaluate side-chains 173 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 VAL 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 948 GLU Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1451 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1584 GLN Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 75 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 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 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 = 0.3673 r_free = 0.3673 target = 0.149850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122132 restraints weight = 10266.196| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.39 r_work: 0.3194 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11420 Z= 0.139 Angle : 0.545 8.729 15659 Z= 0.281 Chirality : 0.041 0.272 1706 Planarity : 0.005 0.086 1814 Dihedral : 17.715 161.116 2182 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.81 % Allowed : 26.52 % Favored : 70.67 % 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: 0.03 (0.24), residues: 1203 helix: 1.06 (0.27), residues: 351 sheet: -0.96 (0.35), residues: 181 loop : -0.17 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1530 HIS 0.003 0.001 HIS A 924 PHE 0.016 0.002 PHE A 805 TYR 0.008 0.001 TYR A1595 ARG 0.013 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 383) hydrogen bonds : angle 5.44288 ( 1165) metal coordination : bond 0.00488 ( 16) metal coordination : angle 2.52481 ( 21) covalent geometry : bond 0.00307 (11404) covalent geometry : angle 0.53762 (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 176 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.084 Fit side-chains REVERT: A 8 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8111 (pt) REVERT: A 69 LYS cc_start: 0.8343 (tttt) cc_final: 0.7972 (tttp) REVERT: A 73 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7155 (mt-10) REVERT: A 114 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: A 123 LYS cc_start: 0.7224 (tttp) cc_final: 0.6814 (tttm) REVERT: A 159 ASP cc_start: 0.7278 (t70) cc_final: 0.7000 (t0) REVERT: A 168 ARG cc_start: 0.8445 (mtm110) cc_final: 0.8118 (mtm-85) REVERT: A 214 GLU cc_start: 0.7652 (tp30) cc_final: 0.7420 (tp30) REVERT: A 290 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7982 (tp) REVERT: A 415 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: A 632 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6677 (tppp) REVERT: A 659 PHE cc_start: 0.6563 (t80) cc_final: 0.6107 (t80) REVERT: A 677 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 748 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5865 (tm-30) REVERT: A 773 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: A 781 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7331 (mp0) REVERT: A 830 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7665 (t80) REVERT: A 1570 PHE cc_start: 0.7776 (p90) cc_final: 0.7376 (p90) REVERT: A 1600 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: A 1617 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7667 (p90) REVERT: A 1644 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7421 (ptm-80) outliers start: 30 outliers final: 14 residues processed: 165 average time/residue: 1.3996 time to fit residues: 247.8217 Evaluate side-chains 167 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 170 VAL Chi-restraints excluded: chain A residue 210 THR 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 517 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1584 GLN Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1644 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 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 ** 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 A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.148785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120502 restraints weight = 10147.699| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.41 r_work: 0.3186 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11420 Z= 0.137 Angle : 0.541 8.845 15659 Z= 0.279 Chirality : 0.041 0.272 1706 Planarity : 0.005 0.070 1814 Dihedral : 17.670 162.281 2182 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.81 % Allowed : 26.34 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1203 helix: 1.17 (0.28), residues: 351 sheet: -0.77 (0.36), residues: 181 loop : -0.12 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1530 HIS 0.003 0.001 HIS A 924 PHE 0.015 0.002 PHE A 805 TYR 0.008 0.001 TYR A1590 ARG 0.013 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 383) hydrogen bonds : angle 5.35767 ( 1165) metal coordination : bond 0.00510 ( 16) metal coordination : angle 2.51817 ( 21) covalent geometry : bond 0.00303 (11404) covalent geometry : angle 0.53369 (15638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8188.97 seconds wall clock time: 142 minutes 9.23 seconds (8529.23 seconds total)