Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 01:54:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y81_33677/04_2023/7y81_33677.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y81_33677/04_2023/7y81_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y81_33677/04_2023/7y81_33677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y81_33677/04_2023/7y81_33677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y81_33677/04_2023/7y81_33677.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y81_33677/04_2023/7y81_33677.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A PHE 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A GLU 1474": "OE1" <-> "OE2" Residue "A PHE 1633": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11044 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9871 Classifications: {'peptide': 1223} Link IDs: {'PTRANS': 57, 'TRANS': 1165} Chain breaks: 9 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1, ' ZN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5559 SG CYS A 750 16.364 55.912 74.661 1.00 60.87 S ATOM 5572 SG CYS A 752 19.374 57.335 76.428 1.00 46.81 S ATOM 5594 SG CYS A 755 19.800 54.173 74.505 1.00 46.28 S ATOM 3484 SG CYS A 491 27.123 52.899 47.829 1.00 56.05 S ATOM 3552 SG CYS A 501 27.375 53.613 44.369 1.00 42.85 S ATOM 3566 SG CYS A 503 29.995 55.155 46.413 1.00 43.99 S ATOM 3588 SG CYS A 506 30.124 51.342 46.034 1.00 41.71 S ATOM 7485 SG CYS A1018 19.155 40.566 107.931 1.00 37.91 S ATOM 7681 SG CYS A1406 16.821 41.452 105.025 1.00 27.11 S ATOM 7732 SG CYS A1414 18.500 44.019 107.321 1.00 29.63 S ATOM 7749 SG CYS A1417 20.643 42.384 104.854 1.00 46.17 S ATOM 668 SG CYS A 88 36.834 43.752 17.551 1.00 58.67 S ATOM 939 SG CYS A 121 37.795 41.575 14.500 1.00 73.50 S ATOM 985 SG CYS A 127 39.732 41.241 17.690 1.00 55.95 S ATOM 1009 SG CYS A 130 36.159 40.052 17.526 1.00 59.89 S Time building chain proxies: 6.44, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 4.91 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1406 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 88 " Number of angles added : 21 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 19 sheets defined 31.0% alpha, 26.7% beta 13 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.293A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.610A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 269 through 287 removed outlier: 3.550A pdb=" N ASN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 4.359A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 373 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.501A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 624 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 658 through 664 removed outlier: 3.953A pdb=" N GLU A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.715A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.539A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.697A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.960A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 Processing helix chain 'A' and resid 1493 through 1501 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.924A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.581A pdb=" N LYS A1593 " --> pdb=" O GLU A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.632A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1667 Processing helix chain 'A' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.883A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.774A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.511A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.637A pdb=" N VAL A 85 " --> pdb=" O TRP A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 5.912A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.206A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.206A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.526A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 533 removed outlier: 10.417A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.713A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.713A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.192A pdb=" N ILE A 700 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 803 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB5, first strand: chain 'A' and resid 1642 through 1643 removed outlier: 6.746A pdb=" N ILE A 920 " --> pdb=" O TRP A1688 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.264A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA A1434 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASP A1521 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR A1436 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER A1519 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A1438 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 5.260A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU A1567 " --> pdb=" O VAL A1582 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.168A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 989 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1421 through 1422 390 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1874 1.32 - 1.44: 3281 1.44 - 1.57: 6103 1.57 - 1.69: 104 1.69 - 1.81: 42 Bond restraints: 11404 Sorted by residual: bond pdb=" O3' U B 34 " pdb=" P A B 35 " ideal model delta sigma weight residual 1.607 1.514 0.093 1.50e-02 4.44e+03 3.84e+01 bond pdb=" O3' C B 45 " pdb=" P U B 46 " ideal model delta sigma weight residual 1.607 1.521 0.086 1.50e-02 4.44e+03 3.28e+01 bond pdb=" O3' U B 46 " pdb=" P G B 47 " ideal model delta sigma weight residual 1.607 1.544 0.063 1.50e-02 4.44e+03 1.77e+01 bond pdb=" C PRO A1641 " pdb=" O PRO A1641 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.16e-02 7.43e+03 8.08e+00 bond pdb=" O3' C B 36 " pdb=" P C B 37 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.50e-02 4.44e+03 7.67e+00 ... (remaining 11399 not shown) Histogram of bond angle deviations from ideal: 89.22 - 98.21: 5 98.21 - 107.20: 701 107.20 - 116.19: 7217 116.19 - 125.19: 7320 125.19 - 134.18: 395 Bond angle restraints: 15638 Sorted by residual: angle pdb=" O2' C B 36 " pdb=" C2' C B 36 " pdb=" C1' C B 36 " ideal model delta sigma weight residual 108.40 89.22 19.18 1.50e+00 4.44e-01 1.64e+02 angle pdb=" C4' U B 46 " pdb=" C3' U B 46 " pdb=" O3' U B 46 " ideal model delta sigma weight residual 109.40 91.58 17.82 1.50e+00 4.44e-01 1.41e+02 angle pdb=" C4' G B 47 " pdb=" C3' G B 47 " pdb=" O3' G B 47 " ideal model delta sigma weight residual 109.40 92.46 16.94 1.50e+00 4.44e-01 1.28e+02 angle pdb=" C4' C B 36 " pdb=" C3' C B 36 " pdb=" O3' C B 36 " ideal model delta sigma weight residual 113.00 128.95 -15.95 1.50e+00 4.44e-01 1.13e+02 angle pdb=" C4' A B 35 " pdb=" C3' A B 35 " pdb=" O3' A B 35 " ideal model delta sigma weight residual 109.40 95.53 13.87 1.50e+00 4.44e-01 8.55e+01 ... (remaining 15633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 6343 35.35 - 70.70: 328 70.70 - 106.05: 28 106.05 - 141.40: 1 141.40 - 176.75: 1 Dihedral angle restraints: 6701 sinusoidal: 3212 harmonic: 3489 Sorted by residual: dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 55.25 176.75 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASN A1449 " pdb=" C ASN A1449 " pdb=" N PRO A1450 " pdb=" CA PRO A1450 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ALA A 721 " pdb=" C ALA A 721 " pdb=" N VAL A 722 " pdb=" CA VAL A 722 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 6698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 1686 0.196 - 0.392: 18 0.392 - 0.588: 1 0.588 - 0.784: 0 0.784 - 0.980: 1 Chirality restraints: 1706 Sorted by residual: chirality pdb=" C2' A B 35 " pdb=" C3' A B 35 " pdb=" O2' A B 35 " pdb=" C1' A B 35 " both_signs ideal model delta sigma weight residual False -2.52 -1.54 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" C2' G B 47 " pdb=" C3' G B 47 " pdb=" O2' G B 47 " pdb=" C1' G B 47 " both_signs ideal model delta sigma weight residual False -2.52 -2.07 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C3' C B 36 " pdb=" C4' C B 36 " pdb=" O3' C B 36 " pdb=" C2' C B 36 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 1703 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 35 " 0.084 2.00e-02 2.50e+03 4.14e-02 4.70e+01 pdb=" N9 A B 35 " -0.105 2.00e-02 2.50e+03 pdb=" C8 A B 35 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A B 35 " 0.012 2.00e-02 2.50e+03 pdb=" C5 A B 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 35 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A B 35 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A B 35 " 0.010 2.00e-02 2.50e+03 pdb=" C2 A B 35 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A B 35 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A B 35 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " 0.049 2.00e-02 2.50e+03 2.33e-02 1.63e+01 pdb=" N9 G B 47 " -0.058 2.00e-02 2.50e+03 pdb=" C8 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G B 47 " 0.014 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G B 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G B 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G B 47 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 45 " 0.047 2.00e-02 2.50e+03 2.40e-02 1.29e+01 pdb=" N1 C B 45 " -0.050 2.00e-02 2.50e+03 pdb=" C2 C B 45 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C B 45 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C B 45 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B 45 " 0.020 2.00e-02 2.50e+03 pdb=" C5 C B 45 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C B 45 " -0.007 2.00e-02 2.50e+03 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 166 2.61 - 3.18: 8521 3.18 - 3.75: 20294 3.75 - 4.33: 28626 4.33 - 4.90: 44530 Nonbonded interactions: 102137 Sorted by model distance: nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 2.034 2.170 nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 2.044 2.170 nonbonded pdb=" O ILE A 940 " pdb=" OH TYR A1425 " model vdw 2.256 2.440 nonbonded pdb=" O GLU A1460 " pdb=" O2' C B 49 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR A 922 " pdb=" OH TYR A1663 " model vdw 2.280 2.440 ... (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 ========== 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: 1.060 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: 4.850 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 38.890 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 11404 Z= 0.351 Angle : 0.858 19.184 15638 Z= 0.489 Chirality : 0.060 0.980 1706 Planarity : 0.008 0.086 1814 Dihedral : 19.330 176.753 4467 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.21), residues: 1203 helix: -2.27 (0.20), residues: 341 sheet: -0.95 (0.35), residues: 196 loop : -0.66 (0.22), residues: 666 *********************** 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 fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.345 Fit side-chains outliers start: 31 outliers final: 24 residues processed: 166 average time/residue: 1.3345 time to fit residues: 238.5321 Evaluate side-chains 158 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 4 average time/residue: 0.5844 time to fit residues: 4.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11404 Z= 0.217 Angle : 0.556 10.295 15638 Z= 0.296 Chirality : 0.044 0.390 1706 Planarity : 0.005 0.064 1814 Dihedral : 12.887 172.270 1980 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer Outliers : 4.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1203 helix: -0.51 (0.25), residues: 348 sheet: -0.72 (0.36), residues: 182 loop : -0.42 (0.22), residues: 673 *********************** 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 190 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 138 time to evaluate : 1.245 Fit side-chains outliers start: 52 outliers final: 29 residues processed: 182 average time/residue: 1.4189 time to fit residues: 277.1090 Evaluate side-chains 160 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.5402 time to fit residues: 4.2500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 11404 Z= 0.303 Angle : 0.576 8.199 15638 Z= 0.302 Chirality : 0.044 0.342 1706 Planarity : 0.005 0.059 1814 Dihedral : 12.898 166.681 1980 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 5.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1203 helix: 0.26 (0.26), residues: 351 sheet: -0.85 (0.36), residues: 182 loop : -0.32 (0.23), residues: 670 *********************** 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 207 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 147 time to evaluate : 1.413 Fit side-chains outliers start: 60 outliers final: 26 residues processed: 196 average time/residue: 1.4340 time to fit residues: 301.2509 Evaluate side-chains 171 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 3 average time/residue: 1.0920 time to fit residues: 5.2619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 0.0060 chunk 121 optimal weight: 0.0270 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 0.3152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS A1649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 11404 Z= 0.152 Angle : 0.501 7.484 15638 Z= 0.264 Chirality : 0.041 0.315 1706 Planarity : 0.004 0.054 1814 Dihedral : 12.875 168.938 1980 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 4.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1203 helix: 0.83 (0.27), residues: 347 sheet: -0.80 (0.36), residues: 178 loop : -0.22 (0.23), residues: 678 *********************** 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 199 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 149 time to evaluate : 1.280 Fit side-chains outliers start: 50 outliers final: 27 residues processed: 187 average time/residue: 1.4119 time to fit residues: 283.5901 Evaluate side-chains 166 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 0.6928 time to fit residues: 4.1682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 286 GLN A 616 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS A1671 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11404 Z= 0.268 Angle : 0.544 7.550 15638 Z= 0.283 Chirality : 0.043 0.323 1706 Planarity : 0.004 0.055 1814 Dihedral : 12.863 167.098 1980 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 4.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.23), residues: 1203 helix: 0.88 (0.27), residues: 351 sheet: -0.82 (0.34), residues: 191 loop : -0.14 (0.24), residues: 661 *********************** 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 190 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 142 time to evaluate : 1.232 Fit side-chains outliers start: 48 outliers final: 30 residues processed: 180 average time/residue: 1.3971 time to fit residues: 270.4079 Evaluate side-chains 169 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 3 average time/residue: 1.1185 time to fit residues: 5.3318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 286 GLN A 616 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1568 HIS A1617 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11404 Z= 0.200 Angle : 0.511 7.496 15638 Z= 0.268 Chirality : 0.042 0.280 1706 Planarity : 0.004 0.054 1814 Dihedral : 12.877 167.291 1980 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 4.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1203 helix: 1.08 (0.28), residues: 351 sheet: -0.78 (0.35), residues: 181 loop : -0.13 (0.24), residues: 671 *********************** 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 189 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 1.411 Fit side-chains outliers start: 43 outliers final: 33 residues processed: 183 average time/residue: 1.3838 time to fit residues: 272.7868 Evaluate side-chains 171 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 29 residues processed: 4 average time/residue: 0.9359 time to fit residues: 5.8668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 616 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 11404 Z= 0.269 Angle : 0.547 7.920 15638 Z= 0.285 Chirality : 0.043 0.261 1706 Planarity : 0.004 0.059 1814 Dihedral : 12.885 165.844 1980 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1203 helix: 0.96 (0.27), residues: 351 sheet: -0.83 (0.36), residues: 173 loop : -0.13 (0.24), residues: 679 *********************** 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 187 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 1.323 Fit side-chains outliers start: 44 outliers final: 32 residues processed: 179 average time/residue: 1.5527 time to fit residues: 299.7257 Evaluate side-chains 171 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 5 average time/residue: 0.7989 time to fit residues: 6.2122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11404 Z= 0.182 Angle : 0.512 7.895 15638 Z= 0.267 Chirality : 0.041 0.259 1706 Planarity : 0.004 0.054 1814 Dihedral : 12.887 166.848 1980 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1203 helix: 1.13 (0.27), residues: 351 sheet: -0.78 (0.35), residues: 181 loop : -0.08 (0.24), residues: 671 *********************** 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 183 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 1.327 Fit side-chains outliers start: 41 outliers final: 29 residues processed: 178 average time/residue: 1.4170 time to fit residues: 271.7773 Evaluate side-chains 166 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 0.1827 time to fit residues: 2.2779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 68 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 102 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11404 Z= 0.178 Angle : 0.511 8.165 15638 Z= 0.265 Chirality : 0.041 0.253 1706 Planarity : 0.004 0.072 1814 Dihedral : 12.879 167.910 1980 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1203 helix: 1.12 (0.27), residues: 357 sheet: -0.72 (0.35), residues: 181 loop : -0.03 (0.24), residues: 665 *********************** 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 177 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.381 Fit side-chains outliers start: 36 outliers final: 32 residues processed: 173 average time/residue: 1.3872 time to fit residues: 258.6066 Evaluate side-chains 169 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 0.9994 time to fit residues: 6.2275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11404 Z= 0.211 Angle : 0.525 8.754 15638 Z= 0.273 Chirality : 0.042 0.251 1706 Planarity : 0.005 0.083 1814 Dihedral : 12.879 167.556 1980 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1203 helix: 1.06 (0.27), residues: 357 sheet: -0.70 (0.35), residues: 181 loop : -0.02 (0.24), residues: 665 ********************** 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 168 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.116 Fit side-chains outliers start: 31 outliers final: 31 residues processed: 166 average time/residue: 1.3903 time to fit residues: 248.5677 Evaluate side-chains 166 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 3 average time/residue: 0.7115 time to fit residues: 4.1744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119866 restraints weight = 10176.963| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.32 r_work: 0.3157 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 11404 Z= 0.250 Angle : 0.545 9.163 15638 Z= 0.283 Chirality : 0.042 0.253 1706 Planarity : 0.005 0.086 1814 Dihedral : 12.888 165.946 1980 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1203 helix: 0.96 (0.27), residues: 357 sheet: -0.74 (0.36), residues: 175 loop : -0.04 (0.24), residues: 671 =============================================================================== Job complete usr+sys time: 4574.82 seconds wall clock time: 82 minutes 12.69 seconds (4932.69 seconds total)