Starting phenix.real_space_refine on Fri Sep 11 20:06:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y81_33677/09_2026/7y81_33677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y81_33677/09_2026/7y81_33677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y81_33677/09_2026/7y81_33677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y81_33677/09_2026/7y81_33677.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y81_33677/09_2026/7y81_33677.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y81_33677/09_2026/7y81_33677.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y81_33677/09_2026/7y81_33677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y81_33677/09_2026/7y81_33677.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.280 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 6810 2.51 5 N 1927 2.21 5 O 2216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11044 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9871 Classifications: {'peptide': 1223} Link IDs: {'PTRANS': 57, 'TRANS': 1165} Chain breaks: 9 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNAv2': 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: {'RNAv2': 19} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1, ' ZN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5559 SG CYS A 750 16.364 55.912 74.661 1.00 60.87 S ATOM 5572 SG CYS A 752 19.374 57.335 76.428 1.00 46.81 S ATOM 5594 SG CYS A 755 19.800 54.173 74.505 1.00 46.28 S ATOM 3484 SG CYS A 491 27.123 52.899 47.829 1.00 56.05 S ATOM 3552 SG CYS A 501 27.375 53.613 44.369 1.00 42.85 S ATOM 3566 SG CYS A 503 29.995 55.155 46.413 1.00 43.99 S ATOM 3588 SG CYS A 506 30.124 51.342 46.034 1.00 41.71 S ATOM 7485 SG CYS A1018 19.155 40.566 107.931 1.00 37.91 S ATOM 7681 SG CYS A1406 16.821 41.452 105.025 1.00 27.11 S ATOM 7732 SG CYS A1414 18.500 44.019 107.321 1.00 29.63 S ATOM 7749 SG CYS A1417 20.643 42.384 104.854 1.00 46.17 S ATOM 668 SG CYS A 88 36.834 43.752 17.551 1.00 58.67 S ATOM 939 SG CYS A 121 37.795 41.575 14.500 1.00 73.50 S ATOM 985 SG CYS A 127 39.732 41.241 17.690 1.00 55.95 S ATOM 1009 SG CYS A 130 36.159 40.052 17.526 1.00 59.89 S Time building chain proxies: 2.64, per 1000 atoms: 0.24 Number of scatterers: 11044 At special positions: 0 Unit cell: (75.9, 81.4, 156.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 31 16.00 P 55 15.00 Mg 1 11.99 O 2216 8.00 N 1927 7.00 C 6810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 561.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1406 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 88 " Number of angles added : 21 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 19 sheets defined 31.0% alpha, 26.7% beta 13 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.293A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.610A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 269 through 287 removed outlier: 3.550A pdb=" N ASN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 4.359A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 373 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.501A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 624 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 658 through 664 removed outlier: 3.953A pdb=" N GLU A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.715A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.539A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.697A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.960A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 Processing helix chain 'A' and resid 1493 through 1501 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.924A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.581A pdb=" N LYS A1593 " --> pdb=" O GLU A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.632A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1667 Processing helix chain 'A' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.883A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.774A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.511A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.637A pdb=" N VAL A 85 " --> pdb=" O TRP A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 5.912A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.206A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.206A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.526A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 533 removed outlier: 10.417A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.713A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.713A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.192A pdb=" N ILE A 700 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 803 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB5, first strand: chain 'A' and resid 1642 through 1643 removed outlier: 6.746A pdb=" N ILE A 920 " --> pdb=" O TRP A1688 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.264A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA A1434 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASP A1521 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR A1436 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER A1519 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A1438 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 5.260A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU A1567 " --> pdb=" O VAL A1582 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.168A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 989 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1421 through 1422 390 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.16 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 1.20e-02 6.94e+03 6.00e+01 bond pdb=" O3' C B 45 " pdb=" P U B 46 " ideal model delta sigma weight residual 1.607 1.521 0.086 1.20e-02 6.94e+03 5.13e+01 bond pdb=" O3' U B 46 " pdb=" P G B 47 " ideal model delta sigma weight residual 1.607 1.544 0.063 1.20e-02 6.94e+03 2.77e+01 bond pdb=" O3' C B 36 " pdb=" P C B 37 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.20e-02 6.94e+03 1.20e+01 bond pdb=" O3' A B 35 " pdb=" P C B 36 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.20e-02 6.94e+03 1.17e+01 ... (remaining 11399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 15527 4.18 - 8.37: 97 8.37 - 12.55: 7 12.55 - 16.73: 3 16.73 - 20.92: 4 Bond angle restraints: 15638 Sorted by residual: angle pdb=" C4' G B 47 " pdb=" C3' G B 47 " pdb=" O3' G B 47 " ideal model delta sigma weight residual 112.50 92.46 20.04 2.00e+00 2.50e-01 1.00e+02 angle pdb=" C4' A B 35 " pdb=" C3' A B 35 " pdb=" O3' A B 35 " ideal model delta sigma weight residual 112.50 95.53 16.97 2.00e+00 2.50e-01 7.20e+01 angle pdb=" O3' G B 47 " pdb=" C3' G B 47 " pdb=" C2' G B 47 " ideal model delta sigma weight residual 113.80 98.01 15.79 2.00e+00 2.50e-01 6.24e+01 angle pdb=" O2' A B 35 " pdb=" C2' A B 35 " pdb=" C1' A B 35 " ideal model delta sigma weight residual 108.20 123.66 -15.46 2.00e+00 2.50e-01 5.98e+01 angle pdb=" C4' U B 46 " pdb=" C3' U B 46 " pdb=" O3' U B 46 " ideal model delta sigma weight residual 112.50 91.58 20.92 3.00e+00 1.11e-01 4.86e+01 ... (remaining 15633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5363 17.89 - 35.77: 885 35.77 - 53.66: 302 53.66 - 71.55: 125 71.55 - 89.44: 26 Dihedral angle restraints: 6701 sinusoidal: 3212 harmonic: 3489 Sorted by residual: dihedral pdb=" C4' G B 33 " pdb=" C3' G B 33 " pdb=" C2' G B 33 " pdb=" C1' G B 33 " ideal model delta sinusoidal sigma weight residual 36.34 -37.64 73.99 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' C B 50 " pdb=" C3' C B 50 " pdb=" C2' C B 50 " pdb=" C1' C B 50 " ideal model delta sinusoidal sigma weight residual 36.34 -37.25 73.60 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' G B 32 " pdb=" C3' G B 32 " pdb=" C2' G B 32 " pdb=" C1' G B 32 " ideal model delta sinusoidal sigma weight residual 36.34 -36.69 73.03 1 3.10e+00 1.04e-01 7.07e+02 ... (remaining 6698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 1663 0.250 - 0.501: 39 0.501 - 0.751: 3 0.751 - 1.001: 0 1.001 - 1.251: 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 -2.79 -1.54 -1.25 2.00e-01 2.50e+01 3.91e+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 -2.79 -2.07 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C3' G B 47 " pdb=" C4' G B 47 " pdb=" O3' G B 47 " pdb=" C2' G B 47 " both_signs ideal model delta sigma weight residual False -2.50 -3.09 0.59 2.00e-01 2.50e+01 8.83e+00 ... (remaining 1703 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 35 " 0.084 2.00e-02 2.50e+03 4.14e-02 4.70e+01 pdb=" N9 A B 35 " -0.105 2.00e-02 2.50e+03 pdb=" C8 A B 35 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A B 35 " 0.012 2.00e-02 2.50e+03 pdb=" C5 A B 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 35 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A B 35 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A B 35 " 0.010 2.00e-02 2.50e+03 pdb=" C2 A B 35 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A B 35 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A B 35 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " 0.049 2.00e-02 2.50e+03 2.33e-02 1.63e+01 pdb=" N9 G B 47 " -0.058 2.00e-02 2.50e+03 pdb=" C8 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G B 47 " 0.014 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G B 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G B 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G B 47 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 45 " 0.047 2.00e-02 2.50e+03 2.40e-02 1.29e+01 pdb=" N1 C B 45 " -0.050 2.00e-02 2.50e+03 pdb=" C2 C B 45 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C B 45 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C B 45 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B 45 " 0.020 2.00e-02 2.50e+03 pdb=" C5 C B 45 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C B 45 " -0.007 2.00e-02 2.50e+03 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 166 2.61 - 3.18: 8521 3.18 - 3.75: 20294 3.75 - 4.33: 28626 4.33 - 4.90: 44530 Nonbonded interactions: 102137 Sorted by model distance: nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 2.034 2.170 nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 2.044 2.170 nonbonded pdb=" O ILE A 940 " pdb=" OH TYR A1425 " model vdw 2.256 3.040 nonbonded pdb=" O GLU A1460 " pdb=" O2' C B 49 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A 922 " pdb=" OH TYR A1663 " model vdw 2.280 3.040 ... (remaining 102132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 11420 Z= 0.272 Angle : 0.985 20.919 15659 Z= 0.476 Chirality : 0.086 1.251 1706 Planarity : 0.008 0.086 1814 Dihedral : 20.904 89.437 4467 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.91 % Allowed : 28.68 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.21), residues: 1203 helix: -2.27 (0.20), residues: 341 sheet: -0.95 (0.35), residues: 196 loop : -0.66 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 193 TYR 0.019 0.002 TYR A 808 PHE 0.025 0.003 PHE A 805 TRP 0.053 0.003 TRP A1530 HIS 0.007 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.27 (11404) covalent geometry : angle 0.97255 / 0.48 (15638) hydrogen bonds : bond 0.23809 / 15.71 ( 383) hydrogen bonds : angle 9.19411 / 6.60 ( 1165) metal coordination : bond 0.00895 / 0.52 ( 16) metal coordination : angle 4.41734 / 2.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.350 Fit side-chains REVERT: A 7 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7120 (m-40) REVERT: A 68 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.7996 (pt) REVERT: A 168 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7928 (mtm-85) REVERT: A 368 LEU cc_start: 0.8077 (mt) cc_final: 0.7794 (mm) REVERT: A 773 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 781 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6965 (mp0) REVERT: A 918 LYS cc_start: 0.6782 (tppp) cc_final: 0.6331 (tptt) outliers start: 31 outliers final: 24 residues processed: 166 average time/residue: 0.5967 time to fit residues: 106.5625 Evaluate side-chains 158 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1502 GLN Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN A 919 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129185 restraints weight = 10432.698| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.46 r_work: 0.3305 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11420 Z= 0.196 Angle : 1.082 24.426 15659 Z= 0.447 Chirality : 0.102 1.112 1706 Planarity : 0.005 0.066 1814 Dihedral : 16.118 147.675 2019 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.03 % Allowed : 25.21 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.22), residues: 1203 helix: -0.59 (0.24), residues: 355 sheet: -0.76 (0.36), residues: 191 loop : -0.50 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 476 TYR 0.014 0.001 TYR A1481 PHE 0.015 0.002 PHE A1520 TRP 0.016 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (11404) covalent geometry : angle 1.07813 / 0.45 (15638) hydrogen bonds : bond 0.05655 / 3.73 ( 383) hydrogen bonds : angle 6.21471 / 4.52 ( 1165) metal coordination : bond 0.00462 / 0.27 ( 16) metal coordination : angle 2.58922 / 1.66 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.410 Fit side-chains REVERT: A 7 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.6933 (m-40) REVERT: A 8 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8090 (pt) REVERT: A 13 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 123 LYS cc_start: 0.6766 (tttp) cc_final: 0.6361 (ttmm) REVERT: A 217 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8053 (tmtm) REVERT: A 238 GLU cc_start: 0.7271 (mp0) cc_final: 0.7005 (mm-30) REVERT: A 290 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7464 (tp) REVERT: A 632 LYS cc_start: 0.6868 (tptt) cc_final: 0.6222 (tppp) REVERT: A 677 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: A 773 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: A 781 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7164 (mp0) REVERT: A 830 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 1502 GLN cc_start: 0.7810 (mt0) cc_final: 0.6324 (mm-40) REVERT: A 1617 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7555 (p90) REVERT: A 1671 ASN cc_start: 0.7282 (t0) cc_final: 0.7011 (t0) outliers start: 43 outliers final: 16 residues processed: 172 average time/residue: 0.6662 time to fit residues: 122.5648 Evaluate side-chains 162 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 172 ILE 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 493 VAL Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.147009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119766 restraints weight = 10276.858| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.32 r_work: 0.3186 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 11420 Z= 0.335 Angle : 1.043 22.027 15659 Z= 0.451 Chirality : 0.094 1.028 1706 Planarity : 0.005 0.062 1814 Dihedral : 16.075 158.033 1999 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.78 % Allowed : 23.52 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.23), residues: 1203 helix: -0.07 (0.26), residues: 352 sheet: -0.93 (0.37), residues: 183 loop : -0.46 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1505 TYR 0.016 0.002 TYR A 702 PHE 0.029 0.003 PHE A 659 TRP 0.017 0.002 TRP A 82 HIS 0.006 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.33 (11404) covalent geometry : angle 1.03704 / 0.45 (15638) hydrogen bonds : bond 0.05659 / 3.68 ( 383) hydrogen bonds : angle 6.16020 / 4.51 ( 1165) metal coordination : bond 0.01122 / 0.76 ( 16) metal coordination : angle 3.27622 / 2.36 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 0.388 Fit side-chains REVERT: A 7 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.6951 (m-40) REVERT: A 114 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: A 123 LYS cc_start: 0.7348 (tttp) cc_final: 0.6935 (tttm) REVERT: A 217 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8246 (tmtm) REVERT: A 274 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7231 (ttp-110) REVERT: A 290 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7950 (tp) REVERT: A 415 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: A 526 GLU cc_start: 0.7856 (mp0) cc_final: 0.7588 (mp0) REVERT: A 677 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: A 773 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 781 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7335 (mp0) REVERT: A 1446 ARG cc_start: 0.7092 (mmp80) cc_final: 0.6625 (mmp80) REVERT: A 1451 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: A 1502 GLN cc_start: 0.8030 (mt0) cc_final: 0.6593 (mm-40) REVERT: A 1595 TYR cc_start: 0.8191 (t80) cc_final: 0.7976 (t80) REVERT: A 1617 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7879 (p90) outliers start: 51 outliers final: 14 residues processed: 190 average time/residue: 0.6566 time to fit residues: 133.2891 Evaluate side-chains 164 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 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 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 1026 SER Chi-restraints excluded: chain A residue 1451 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1617 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.154635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127451 restraints weight = 10266.263| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.39 r_work: 0.3308 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11420 Z= 0.155 Angle : 0.835 17.282 15659 Z= 0.364 Chirality : 0.080 1.046 1706 Planarity : 0.004 0.059 1814 Dihedral : 16.035 161.147 1994 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.94 % Allowed : 24.55 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1203 helix: 0.55 (0.27), residues: 351 sheet: -1.00 (0.36), residues: 185 loop : -0.31 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1505 TYR 0.008 0.001 TYR A1595 PHE 0.017 0.002 PHE A 15 TRP 0.015 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (11404) covalent geometry : angle 0.83044 / 0.36 (15638) hydrogen bonds : bond 0.04235 / 2.75 ( 383) hydrogen bonds : angle 5.75531 / 4.20 ( 1165) metal coordination : bond 0.00518 / 0.27 ( 16) metal coordination : angle 2.51173 / 1.75 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.350 Fit side-chains REVERT: A 69 LYS cc_start: 0.8378 (tttt) cc_final: 0.7977 (tttp) REVERT: A 114 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: A 123 LYS cc_start: 0.7214 (tttp) cc_final: 0.6815 (tttm) REVERT: A 206 THR cc_start: 0.8604 (m) cc_final: 0.8349 (p) REVERT: A 217 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8203 (tttm) REVERT: A 274 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7191 (ttp-110) REVERT: A 677 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: A 748 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5799 (tm-30) REVERT: A 773 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: A 781 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7249 (mp0) REVERT: A 830 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8059 (t80) REVERT: A 1502 GLN cc_start: 0.7902 (mt0) cc_final: 0.6488 (mm-40) REVERT: A 1570 PHE cc_start: 0.7833 (p90) cc_final: 0.7439 (p90) REVERT: A 1600 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: A 1617 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7771 (p90) outliers start: 42 outliers final: 11 residues processed: 183 average time/residue: 0.6678 time to fit residues: 130.3426 Evaluate side-chains 163 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 516 ASP 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 1458 VAL Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1593 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 286 GLN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119522 restraints weight = 10135.923| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.30 r_work: 0.3156 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11420 Z= 0.339 Angle : 1.012 22.127 15659 Z= 0.439 Chirality : 0.092 1.048 1706 Planarity : 0.005 0.062 1814 Dihedral : 16.109 174.259 1988 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.69 % Allowed : 23.52 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1203 helix: 0.37 (0.27), residues: 351 sheet: -1.06 (0.36), residues: 183 loop : -0.35 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1505 TYR 0.015 0.002 TYR A 702 PHE 0.024 0.003 PHE A 659 TRP 0.013 0.002 TRP A 82 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.34 (11404) covalent geometry : angle 1.00610 / 0.44 (15638) hydrogen bonds : bond 0.05288 / 3.44 ( 383) hydrogen bonds : angle 6.00888 / 4.41 ( 1165) metal coordination : bond 0.00994 / 0.62 ( 16) metal coordination : angle 3.11303 / 2.15 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 0.379 Fit side-chains REVERT: A 95 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: A 114 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: A 123 LYS cc_start: 0.7403 (tttp) cc_final: 0.7007 (tttm) REVERT: A 215 HIS cc_start: 0.8094 (t70) cc_final: 0.7884 (t-170) REVERT: A 217 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8185 (tttm) REVERT: A 274 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7196 (ttp-110) REVERT: A 415 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: A 494 SER cc_start: 0.8656 (m) cc_final: 0.8217 (t) REVERT: A 526 GLU cc_start: 0.7840 (mp0) cc_final: 0.7574 (mp0) REVERT: A 659 PHE cc_start: 0.6713 (t80) cc_final: 0.6275 (t80) REVERT: A 677 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: A 748 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: A 1437 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: A 1502 GLN cc_start: 0.7956 (mt0) cc_final: 0.6514 (mm-40) REVERT: A 1528 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8382 (mpp80) REVERT: A 1570 PHE cc_start: 0.7937 (p90) cc_final: 0.7549 (p90) REVERT: A 1600 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: A 1617 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.8059 (p90) outliers start: 50 outliers final: 18 residues processed: 175 average time/residue: 0.6981 time to fit residues: 130.0921 Evaluate side-chains 171 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 114 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 567 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 806 ASP Chi-restraints excluded: chain A residue 855 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1437 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1528 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3741 r_free = 0.3741 target = 0.155796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129902 restraints weight = 10197.004| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.29 r_work: 0.3323 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11420 Z= 0.163 Angle : 0.828 16.538 15659 Z= 0.363 Chirality : 0.078 1.006 1706 Planarity : 0.005 0.058 1814 Dihedral : 16.019 176.261 1988 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.37 % Allowed : 25.12 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1203 helix: 0.86 (0.27), residues: 351 sheet: -1.06 (0.35), residues: 185 loop : -0.28 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 51 TYR 0.008 0.001 TYR A1481 PHE 0.017 0.002 PHE A 15 TRP 0.014 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (11404) covalent geometry : angle 0.82331 / 0.36 (15638) hydrogen bonds : bond 0.04113 / 2.67 ( 383) hydrogen bonds : angle 5.68382 / 4.16 ( 1165) metal coordination : bond 0.00468 / 0.27 ( 16) metal coordination : angle 2.49525 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.379 Fit side-chains REVERT: A 7 ASN cc_start: 0.7480 (m-40) cc_final: 0.6864 (m-40) REVERT: A 8 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8193 (pt) REVERT: A 69 LYS cc_start: 0.8366 (tttt) cc_final: 0.8035 (tttp) REVERT: A 114 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: A 123 LYS cc_start: 0.7342 (tttp) cc_final: 0.6944 (tttm) REVERT: A 168 ARG cc_start: 0.8459 (mtm110) cc_final: 0.8162 (mtm-85) REVERT: A 206 THR cc_start: 0.8669 (m) cc_final: 0.8386 (p) REVERT: A 217 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8121 (tttm) REVERT: A 274 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7212 (ttp-110) REVERT: A 494 SER cc_start: 0.8589 (m) cc_final: 0.8079 (t) REVERT: A 677 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: A 748 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6002 (tm-30) REVERT: A 773 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: A 781 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7244 (mp0) REVERT: A 830 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8098 (t80) REVERT: A 1502 GLN cc_start: 0.7938 (mt0) cc_final: 0.6499 (mm-40) REVERT: A 1570 PHE cc_start: 0.7863 (p90) cc_final: 0.7469 (p90) REVERT: A 1600 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: A 1617 HIS cc_start: 0.8185 (p-80) cc_final: 0.7935 (p90) outliers start: 36 outliers final: 13 residues processed: 178 average time/residue: 0.6674 time to fit residues: 126.7896 Evaluate side-chains 168 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 217 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 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 1584 GLN Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1600 GLU 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 116 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 286 GLN A 696 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120039 restraints weight = 10168.901| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.30 r_work: 0.3191 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11420 Z= 0.330 Angle : 0.987 21.296 15659 Z= 0.431 Chirality : 0.088 0.991 1706 Planarity : 0.006 0.062 1814 Dihedral : 16.120 175.363 1986 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.94 % Allowed : 24.18 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1203 helix: 0.56 (0.27), residues: 351 sheet: -1.06 (0.36), residues: 183 loop : -0.33 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 51 TYR 0.015 0.002 TYR A 702 PHE 0.027 0.003 PHE A 659 TRP 0.012 0.002 TRP A 82 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.33 (11404) covalent geometry : angle 0.98180 / 0.43 (15638) hydrogen bonds : bond 0.05149 / 3.34 ( 383) hydrogen bonds : angle 5.92048 / 4.34 ( 1165) metal coordination : bond 0.01029 / 0.65 ( 16) metal coordination : angle 3.01673 / 2.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.307 Fit side-chains REVERT: A 7 ASN cc_start: 0.7454 (m-40) cc_final: 0.6842 (m-40) REVERT: A 114 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: A 123 LYS cc_start: 0.7378 (tttp) cc_final: 0.6988 (tttm) REVERT: A 159 ASP cc_start: 0.7376 (t70) cc_final: 0.7115 (t70) REVERT: A 217 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8177 (tttm) REVERT: A 274 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7175 (ttp-110) REVERT: A 415 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: A 494 SER cc_start: 0.8674 (m) cc_final: 0.8261 (t) REVERT: A 526 GLU cc_start: 0.7865 (mp0) cc_final: 0.7589 (mp0) REVERT: A 677 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 719 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7172 (mpt-90) REVERT: A 748 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6247 (tm-30) REVERT: A 773 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: A 918 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6828 (tppp) REVERT: A 997 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8506 (mtp) REVERT: A 1024 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: A 1451 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: A 1502 GLN cc_start: 0.7937 (mt0) cc_final: 0.6483 (mm-40) REVERT: A 1570 PHE cc_start: 0.7909 (p90) cc_final: 0.7497 (p90) REVERT: A 1600 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: A 1644 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7450 (ptm-80) outliers start: 42 outliers final: 19 residues processed: 171 average time/residue: 0.6866 time to fit residues: 125.1516 Evaluate side-chains 172 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 567 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 719 ARG Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 855 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1024 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 1514 LYS Chi-restraints excluded: chain A residue 1563 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 1644 ARG Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128434 restraints weight = 10160.523| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.30 r_work: 0.3303 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2511 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= 0.174 Angle : 0.831 17.301 15659 Z= 0.364 Chirality : 0.076 0.966 1706 Planarity : 0.005 0.060 1814 Dihedral : 16.022 172.153 1986 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.91 % Allowed : 25.21 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1203 helix: 0.85 (0.27), residues: 351 sheet: -1.12 (0.34), residues: 185 loop : -0.22 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 51 TYR 0.009 0.001 TYR A1481 PHE 0.018 0.002 PHE A 805 TRP 0.013 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (11404) covalent geometry : angle 0.82715 / 0.36 (15638) hydrogen bonds : bond 0.04152 / 2.69 ( 383) hydrogen bonds : angle 5.65606 / 4.15 ( 1165) metal coordination : bond 0.00533 / 0.31 ( 16) metal coordination : angle 2.42595 / 1.66 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7416 (m-40) cc_final: 0.6818 (m-40) REVERT: A 69 LYS cc_start: 0.8352 (tttt) cc_final: 0.8004 (tttp) REVERT: A 114 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: A 123 LYS cc_start: 0.7389 (tttp) cc_final: 0.6996 (tttm) REVERT: A 214 GLU cc_start: 0.7692 (tp30) cc_final: 0.7483 (tp30) REVERT: A 217 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8133 (tptp) REVERT: A 274 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7182 (ttp-110) REVERT: A 344 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7182 (tttt) REVERT: A 494 SER cc_start: 0.8619 (m) cc_final: 0.8127 (t) REVERT: A 677 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: A 748 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6021 (tm-30) REVERT: A 773 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8047 (mm-30) REVERT: A 781 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7272 (mp0) REVERT: A 830 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8159 (t80) REVERT: A 997 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8382 (mtp) REVERT: A 1502 GLN cc_start: 0.7902 (mt0) cc_final: 0.6487 (mm-40) REVERT: A 1570 PHE cc_start: 0.7849 (p90) cc_final: 0.7443 (p90) REVERT: A 1600 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: A 1617 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7958 (p90) outliers start: 31 outliers final: 17 residues processed: 170 average time/residue: 0.6768 time to fit residues: 122.4405 Evaluate side-chains 170 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 421 ARG 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 997 MET 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 1563 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 1656 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 0.0370 chunk 28 optimal weight: 0.0020 chunk 46 optimal weight: 0.2980 chunk 35 optimal weight: 0.0470 chunk 70 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 overall best weight: 0.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.140798 restraints weight = 10123.677| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.27 r_work: 0.3463 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11420 Z= 0.127 Angle : 0.763 12.579 15659 Z= 0.335 Chirality : 0.070 0.956 1706 Planarity : 0.005 0.058 1814 Dihedral : 15.715 158.860 1986 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.44 % Allowed : 25.68 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1203 helix: 1.36 (0.28), residues: 344 sheet: -0.88 (0.34), residues: 186 loop : -0.10 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 51 TYR 0.008 0.001 TYR A 707 PHE 0.015 0.001 PHE A1520 TRP 0.018 0.001 TRP A 23 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (11404) covalent geometry : angle 0.75827 / 0.33 (15638) hydrogen bonds : bond 0.03661 / 2.38 ( 383) hydrogen bonds : angle 5.30705 / 3.90 ( 1165) metal coordination : bond 0.00372 / 0.23 ( 16) metal coordination : angle 2.44613 / 1.56 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.405 Fit side-chains REVERT: A 69 LYS cc_start: 0.8344 (tttt) cc_final: 0.7946 (tttp) REVERT: A 123 LYS cc_start: 0.7036 (tttp) cc_final: 0.6643 (tttm) REVERT: A 206 THR cc_start: 0.8540 (m) cc_final: 0.8325 (p) REVERT: A 748 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5839 (tm-30) REVERT: A 773 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: A 781 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7236 (mp0) REVERT: A 1502 GLN cc_start: 0.7894 (mt0) cc_final: 0.6462 (mm-40) REVERT: A 1596 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6784 (mm-40) REVERT: A 1600 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: A 1617 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7625 (p90) REVERT: A 1644 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7374 (ptm-80) REVERT: A 1669 LYS cc_start: 0.7196 (ttmt) cc_final: 0.6688 (mtmt) outliers start: 26 outliers final: 10 residues processed: 179 average time/residue: 0.6286 time to fit residues: 120.7361 Evaluate side-chains 157 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1563 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 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 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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** ** A1547 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 = 0.3719 r_free = 0.3719 target = 0.155154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128242 restraints weight = 10254.349| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.39 r_work: 0.3286 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11420 Z= 0.174 Angle : 0.807 14.996 15659 Z= 0.354 Chirality : 0.072 0.943 1706 Planarity : 0.005 0.059 1814 Dihedral : 15.705 160.173 1983 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.59 % Allowed : 26.62 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1203 helix: 1.26 (0.28), residues: 349 sheet: -0.95 (0.33), residues: 194 loop : -0.04 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 51 TYR 0.009 0.001 TYR A1590 PHE 0.017 0.002 PHE A 824 TRP 0.021 0.001 TRP A 82 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (11404) covalent geometry : angle 0.80243 / 0.35 (15638) hydrogen bonds : bond 0.03960 / 2.60 ( 383) hydrogen bonds : angle 5.34488 / 3.93 ( 1165) metal coordination : bond 0.00521 / 0.29 ( 16) metal coordination : angle 2.43732 / 1.55 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.395 Fit side-chains REVERT: A 69 LYS cc_start: 0.8322 (tttt) cc_final: 0.7945 (tttp) REVERT: A 123 LYS cc_start: 0.6997 (tttp) cc_final: 0.6578 (tttm) REVERT: A 168 ARG cc_start: 0.8472 (mtm110) cc_final: 0.8143 (mtm-85) REVERT: A 206 THR cc_start: 0.8595 (m) cc_final: 0.8335 (p) REVERT: A 677 GLU cc_start: 0.7817 (tt0) cc_final: 0.7268 (mp0) REVERT: A 748 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5801 (tm-30) REVERT: A 773 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7928 (mm-30) REVERT: A 830 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.7707 (t80) REVERT: A 1458 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8560 (m) REVERT: A 1502 GLN cc_start: 0.7825 (mt0) cc_final: 0.6397 (mm-40) REVERT: A 1596 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6701 (mm-40) REVERT: A 1600 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: A 1617 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.7567 (p90) REVERT: A 1644 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7385 (ptm-80) REVERT: A 1669 LYS cc_start: 0.7147 (ttmt) cc_final: 0.6693 (mtmt) outliers start: 17 outliers final: 8 residues processed: 155 average time/residue: 0.6807 time to fit residues: 112.6162 Evaluate side-chains 156 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1563 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 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 39 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 0.0980 chunk 102 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 HIS ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.158802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131824 restraints weight = 10144.384| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.39 r_work: 0.3346 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11420 Z= 0.146 Angle : 0.773 14.206 15659 Z= 0.340 Chirality : 0.070 0.966 1706 Planarity : 0.005 0.057 1814 Dihedral : 15.700 162.338 1983 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.69 % Allowed : 26.80 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1203 helix: 1.41 (0.28), residues: 343 sheet: -0.82 (0.34), residues: 192 loop : -0.02 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 51 TYR 0.007 0.001 TYR A 707 PHE 0.014 0.001 PHE A 824 TRP 0.020 0.001 TRP A1530 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (11404) covalent geometry : angle 0.76851 / 0.34 (15638) hydrogen bonds : bond 0.03789 / 2.47 ( 383) hydrogen bonds : angle 5.28411 / 3.88 ( 1165) metal coordination : bond 0.00436 / 0.25 ( 16) metal coordination : angle 2.38533 / 1.55 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3924.73 seconds wall clock time: 67 minutes 52.30 seconds (4072.30 seconds total)