Starting phenix.real_space_refine on Tue Nov 21 23:43:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/11_2023/7oim_12932_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/11_2023/7oim_12932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/11_2023/7oim_12932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/11_2023/7oim_12932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/11_2023/7oim_12932_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oim_12932/11_2023/7oim_12932_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 2 6.06 5 P 8 5.49 5 Mg 1 5.21 5 S 211 5.16 5 C 22671 2.51 5 N 6108 2.21 5 O 6596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3993": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 35597 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 35597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4432, 35597 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1, 'AGS': 1, 'ATP': 1} Classifications: {'peptide': 4426, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 183, 'TRANS': 4242, None: 6} Not linked: pdbres="GLY A5150 " pdbres="ATP A5201 " Not linked: pdbres="ATP A5201 " pdbres=" MG A5202 " Not linked: pdbres=" MG A5202 " pdbres=" ZN A5203 " Not linked: pdbres=" ZN A5203 " pdbres=" ZN A5204 " Not linked: pdbres=" ZN A5204 " pdbres="ADP A5205 " Not linked: pdbres="ADP A5205 " pdbres="AGS A5206 " Chain breaks: 15 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26526 SG CYS A3962 90.965 134.860 220.574 1.00156.31 S ATOM 26690 SG CYS A3982 88.838 133.051 223.422 1.00148.05 S ATOM 26715 SG CYS A3985 92.641 133.384 223.408 1.00156.00 S ATOM 26416 SG CYS A3947 81.021 128.628 219.242 1.00126.19 S ATOM 26441 SG CYS A3950 78.901 125.352 217.540 1.00126.72 S ATOM 26569 SG CYS A3967 78.504 127.837 215.770 1.00139.40 S Time building chain proxies: 19.11, per 1000 atoms: 0.54 Number of scatterers: 35597 At special positions: 0 Unit cell: (129.519, 155.844, 244.296, 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 2 29.99 S 211 16.00 P 8 15.00 Mg 1 11.99 O 6596 8.00 N 6108 7.00 C 22671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 992 " distance=2.03 Simple disulfide: pdb=" SG CYS A2605 " - pdb=" SG CYS A2653 " distance=2.03 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: 13.59 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" ND1 HIS A3964 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3982 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " Number of angles added : 3 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 205 helices and 13 sheets defined 52.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 22.18 Creating SS restraints... Processing helix chain 'A' and resid 493 through 514 removed outlier: 3.545A pdb=" N VAL A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 removed outlier: 3.761A pdb=" N SER A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.590A pdb=" N TRP A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 593 through 603 Processing helix chain 'A' and resid 611 through 617 removed outlier: 3.767A pdb=" N ASP A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Proline residue: A 637 - end of helix Processing helix chain 'A' and resid 644 through 655 Processing helix chain 'A' and resid 663 through 666 Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 760 through 771 Processing helix chain 'A' and resid 781 through 799 Processing helix chain 'A' and resid 811 through 826 Processing helix chain 'A' and resid 835 through 849 removed outlier: 3.817A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 888 removed outlier: 3.500A pdb=" N SER A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 Processing helix chain 'A' and resid 930 through 938 Processing helix chain 'A' and resid 943 through 950 Processing helix chain 'A' and resid 963 through 981 Processing helix chain 'A' and resid 995 through 1009 Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1033 through 1043 Processing helix chain 'A' and resid 1045 through 1048 No H-bonds generated for 'chain 'A' and resid 1045 through 1048' Processing helix chain 'A' and resid 1054 through 1071 Processing helix chain 'A' and resid 1080 through 1088 Processing helix chain 'A' and resid 1090 through 1102 removed outlier: 3.767A pdb=" N ARG A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1142 Processing helix chain 'A' and resid 1155 through 1158 No H-bonds generated for 'chain 'A' and resid 1155 through 1158' Processing helix chain 'A' and resid 1167 through 1170 Processing helix chain 'A' and resid 1191 through 1202 Processing helix chain 'A' and resid 1207 through 1217 Processing helix chain 'A' and resid 1234 through 1240 removed outlier: 3.903A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1263 through 1269 Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'A' and resid 1278 through 1288 Processing helix chain 'A' and resid 1299 through 1328 Processing helix chain 'A' and resid 1339 through 1345 Processing helix chain 'A' and resid 1362 through 1370 removed outlier: 4.299A pdb=" N ALA A1366 " --> pdb=" O GLN A1362 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A1369 " --> pdb=" O LYS A1365 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A1370 " --> pdb=" O ALA A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1386 Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1404 through 1414 removed outlier: 4.090A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1439 removed outlier: 4.592A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1463 removed outlier: 3.682A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1476 Processing helix chain 'A' and resid 1479 through 1486 removed outlier: 4.554A pdb=" N LYS A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1506 Processing helix chain 'A' and resid 1545 through 1557 removed outlier: 3.839A pdb=" N LEU A1557 " --> pdb=" O ASN A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1564 through 1593 Processing helix chain 'A' and resid 1631 through 1657 Processing helix chain 'A' and resid 1662 through 1664 No H-bonds generated for 'chain 'A' and resid 1662 through 1664' Processing helix chain 'A' and resid 1668 through 1677 Processing helix chain 'A' and resid 1685 through 1690 Processing helix chain 'A' and resid 1700 through 1708 Processing helix chain 'A' and resid 1714 through 1725 Processing helix chain 'A' and resid 1737 through 1749 Processing helix chain 'A' and resid 1761 through 1774 Processing helix chain 'A' and resid 1799 through 1801 No H-bonds generated for 'chain 'A' and resid 1799 through 1801' Processing helix chain 'A' and resid 1803 through 1810 removed outlier: 3.631A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1843 Processing helix chain 'A' and resid 1859 through 1861 No H-bonds generated for 'chain 'A' and resid 1859 through 1861' Processing helix chain 'A' and resid 1864 through 1880 Processing helix chain 'A' and resid 1901 through 1904 No H-bonds generated for 'chain 'A' and resid 1901 through 1904' Processing helix chain 'A' and resid 1918 through 1928 Processing helix chain 'A' and resid 1939 through 1941 No H-bonds generated for 'chain 'A' and resid 1939 through 1941' Processing helix chain 'A' and resid 1960 through 1973 Processing helix chain 'A' and resid 1994 through 2002 Processing helix chain 'A' and resid 2028 through 2036 Processing helix chain 'A' and resid 2081 through 2086 removed outlier: 4.481A pdb=" N ASP A2086 " --> pdb=" O PHE A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2121 Processing helix chain 'A' and resid 2123 through 2136 Proline residue: A2128 - end of helix removed outlier: 4.137A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2164 Processing helix chain 'A' and resid 2173 through 2192 Processing helix chain 'A' and resid 2195 through 2202 Processing helix chain 'A' and resid 2208 through 2223 Processing helix chain 'A' and resid 2251 through 2254 No H-bonds generated for 'chain 'A' and resid 2251 through 2254' Processing helix chain 'A' and resid 2309 through 2318 Processing helix chain 'A' and resid 2331 through 2341 Processing helix chain 'A' and resid 2359 through 2373 removed outlier: 4.083A pdb=" N ILE A2364 " --> pdb=" O ASN A2360 " (cutoff:3.500A) Processing helix chain 'A' and resid 2388 through 2399 Processing helix chain 'A' and resid 2418 through 2438 Processing helix chain 'A' and resid 2456 through 2463 removed outlier: 3.813A pdb=" N LEU A2463 " --> pdb=" O ILE A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2499 Processing helix chain 'A' and resid 2522 through 2524 No H-bonds generated for 'chain 'A' and resid 2522 through 2524' Processing helix chain 'A' and resid 2537 through 2539 No H-bonds generated for 'chain 'A' and resid 2537 through 2539' Processing helix chain 'A' and resid 2551 through 2562 Processing helix chain 'A' and resid 2572 through 2588 Processing helix chain 'A' and resid 2606 through 2614 Processing helix chain 'A' and resid 2619 through 2628 Processing helix chain 'A' and resid 2643 through 2653 Processing helix chain 'A' and resid 2661 through 2668 Processing helix chain 'A' and resid 2674 through 2676 No H-bonds generated for 'chain 'A' and resid 2674 through 2676' Processing helix chain 'A' and resid 2679 through 2696 Processing helix chain 'A' and resid 2707 through 2721 Processing helix chain 'A' and resid 2737 through 2746 Processing helix chain 'A' and resid 2757 through 2759 No H-bonds generated for 'chain 'A' and resid 2757 through 2759' Processing helix chain 'A' and resid 2776 through 2790 Processing helix chain 'A' and resid 2807 through 2809 No H-bonds generated for 'chain 'A' and resid 2807 through 2809' Processing helix chain 'A' and resid 2817 through 2819 No H-bonds generated for 'chain 'A' and resid 2817 through 2819' Processing helix chain 'A' and resid 2821 through 2824 No H-bonds generated for 'chain 'A' and resid 2821 through 2824' Processing helix chain 'A' and resid 2868 through 2877 Processing helix chain 'A' and resid 2884 through 2888 Processing helix chain 'A' and resid 2892 through 2906 Processing helix chain 'A' and resid 2914 through 2931 Processing helix chain 'A' and resid 2937 through 2947 Processing helix chain 'A' and resid 2956 through 2962 Processing helix chain 'A' and resid 2975 through 2983 Processing helix chain 'A' and resid 3011 through 3018 Processing helix chain 'A' and resid 3038 through 3055 Processing helix chain 'A' and resid 3074 through 3076 No H-bonds generated for 'chain 'A' and resid 3074 through 3076' Processing helix chain 'A' and resid 3113 through 3118 Processing helix chain 'A' and resid 3123 through 3127 removed outlier: 3.512A pdb=" N ARG A3127 " --> pdb=" O PRO A3123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3123 through 3127' Processing helix chain 'A' and resid 3141 through 3158 Processing helix chain 'A' and resid 3173 through 3176 No H-bonds generated for 'chain 'A' and resid 3173 through 3176' Processing helix chain 'A' and resid 3184 through 3196 Processing helix chain 'A' and resid 3204 through 3220 removed outlier: 3.805A pdb=" N LYS A3208 " --> pdb=" O GLU A3204 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS A3220 " --> pdb=" O ILE A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3223 through 3231 removed outlier: 4.878A pdb=" N SER A3230 " --> pdb=" O VAL A3226 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLY A3231 " --> pdb=" O VAL A3227 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3248 Processing helix chain 'A' and resid 3255 through 3263 Processing helix chain 'A' and resid 3288 through 3295 Processing helix chain 'A' and resid 3314 through 3325 Processing helix chain 'A' and resid 3349 through 3364 Processing helix chain 'A' and resid 3414 through 3419 Processing helix chain 'A' and resid 3423 through 3426 Processing helix chain 'A' and resid 3477 through 3491 removed outlier: 5.012A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET A3491 " --> pdb=" O GLY A3487 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3511 Processing helix chain 'A' and resid 3518 through 3539 Processing helix chain 'A' and resid 3549 through 3554 Processing helix chain 'A' and resid 3557 through 3563 Processing helix chain 'A' and resid 3566 through 3589 Proline residue: A3580 - end of helix Processing helix chain 'A' and resid 3596 through 3599 No H-bonds generated for 'chain 'A' and resid 3596 through 3599' Processing helix chain 'A' and resid 3605 through 3614 Processing helix chain 'A' and resid 3658 through 3675 Processing helix chain 'A' and resid 3681 through 3690 Processing helix chain 'A' and resid 3693 through 3698 Processing helix chain 'A' and resid 3703 through 3721 Processing helix chain 'A' and resid 3728 through 3745 Processing helix chain 'A' and resid 3763 through 3783 removed outlier: 7.657A pdb=" N THR A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A3774 " --> pdb=" O HIS A3770 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A3778 " --> pdb=" O ARG A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3799 removed outlier: 5.775A pdb=" N ALA A3796 " --> pdb=" O SER A3793 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS A3799 " --> pdb=" O ALA A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3808 through 3823 removed outlier: 3.884A pdb=" N ASP A3823 " --> pdb=" O MET A3819 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3838 Processing helix chain 'A' and resid 3840 through 3846 Processing helix chain 'A' and resid 3857 through 3889 removed outlier: 5.225A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3895 through 3909 removed outlier: 4.077A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3918 through 3940 Processing helix chain 'A' and resid 3968 through 3974 Processing helix chain 'A' and resid 4001 through 4025 Processing helix chain 'A' and resid 4036 through 4044 Processing helix chain 'A' and resid 4083 through 4088 Processing helix chain 'A' and resid 4093 through 4095 No H-bonds generated for 'chain 'A' and resid 4093 through 4095' Processing helix chain 'A' and resid 4097 through 4110 Processing helix chain 'A' and resid 4117 through 4137 Processing helix chain 'A' and resid 4143 through 4155 Processing helix chain 'A' and resid 4172 through 4197 removed outlier: 3.643A pdb=" N GLU A4197 " --> pdb=" O SER A4193 " (cutoff:3.500A) Processing helix chain 'A' and resid 4205 through 4218 Processing helix chain 'A' and resid 4223 through 4235 Processing helix chain 'A' and resid 4238 through 4245 Processing helix chain 'A' and resid 4252 through 4254 No H-bonds generated for 'chain 'A' and resid 4252 through 4254' Processing helix chain 'A' and resid 4257 through 4261 removed outlier: 4.281A pdb=" N ALA A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4257 through 4261' Processing helix chain 'A' and resid 4272 through 4275 removed outlier: 3.847A pdb=" N VAL A4275 " --> pdb=" O ARG A4272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4272 through 4275' Processing helix chain 'A' and resid 4280 through 4292 Processing helix chain 'A' and resid 4297 through 4304 Processing helix chain 'A' and resid 4310 through 4330 Processing helix chain 'A' and resid 4343 through 4352 Processing helix chain 'A' and resid 4359 through 4369 removed outlier: 3.743A pdb=" N SER A4367 " --> pdb=" O CYS A4363 " (cutoff:3.500A) Processing helix chain 'A' and resid 4385 through 4402 Processing helix chain 'A' and resid 4406 through 4416 Proline residue: A4410 - end of helix removed outlier: 4.218A pdb=" N PHE A4416 " --> pdb=" O ASN A4413 " (cutoff:3.500A) Processing helix chain 'A' and resid 4418 through 4420 No H-bonds generated for 'chain 'A' and resid 4418 through 4420' Processing helix chain 'A' and resid 4523 through 4543 removed outlier: 3.930A pdb=" N HIS A4543 " --> pdb=" O VAL A4539 " (cutoff:3.500A) Processing helix chain 'A' and resid 4545 through 4551 Processing helix chain 'A' and resid 4560 through 4577 Processing helix chain 'A' and resid 4582 through 4595 Processing helix chain 'A' and resid 4614 through 4634 removed outlier: 4.674A pdb=" N HIS A4634 " --> pdb=" O ARG A4630 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4647 Processing helix chain 'A' and resid 4656 through 4659 No H-bonds generated for 'chain 'A' and resid 4656 through 4659' Processing helix chain 'A' and resid 4666 through 4668 No H-bonds generated for 'chain 'A' and resid 4666 through 4668' Processing helix chain 'A' and resid 4692 through 4701 Processing helix chain 'A' and resid 4709 through 4716 Processing helix chain 'A' and resid 4718 through 4740 removed outlier: 4.521A pdb=" N LEU A4723 " --> pdb=" O ALA A4719 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A4724 " --> pdb=" O GLU A4720 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS A4725 " --> pdb=" O LEU A4721 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE A4726 " --> pdb=" O ARG A4722 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A4727 " --> pdb=" O LEU A4723 " (cutoff:3.500A) Proline residue: A4728 - end of helix Processing helix chain 'A' and resid 4752 through 4756 Processing helix chain 'A' and resid 4762 through 4782 Processing helix chain 'A' and resid 4786 through 4789 No H-bonds generated for 'chain 'A' and resid 4786 through 4789' Processing helix chain 'A' and resid 4821 through 4844 Processing helix chain 'A' and resid 4860 through 4862 No H-bonds generated for 'chain 'A' and resid 4860 through 4862' Processing helix chain 'A' and resid 4873 through 4879 removed outlier: 3.806A pdb=" N ASN A4879 " --> pdb=" O LEU A4875 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4904 Processing helix chain 'A' and resid 4931 through 4940 Processing helix chain 'A' and resid 4948 through 4956 removed outlier: 3.930A pdb=" N SER A4952 " --> pdb=" O ASN A4948 " (cutoff:3.500A) Processing helix chain 'A' and resid 4961 through 4979 Processing helix chain 'A' and resid 4989 through 4993 Processing helix chain 'A' and resid 5004 through 5012 removed outlier: 5.209A pdb=" N ARG A5012 " --> pdb=" O LYS A5008 " (cutoff:3.500A) Processing helix chain 'A' and resid 5015 through 5035 removed outlier: 3.851A pdb=" N ILE A5018 " --> pdb=" O LEU A5015 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A5019 " --> pdb=" O ARG A5016 " (cutoff:3.500A) Processing helix chain 'A' and resid 5046 through 5048 No H-bonds generated for 'chain 'A' and resid 5046 through 5048' Processing helix chain 'A' and resid 5054 through 5066 removed outlier: 4.180A pdb=" N GLU A5066 " --> pdb=" O THR A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5069 through 5083 removed outlier: 4.739A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5099 through 5108 Processing helix chain 'A' and resid 5116 through 5120 Processing helix chain 'A' and resid 5132 through 5148 Processing sheet with id= A, first strand: chain 'A' and resid 1149 through 1151 Processing sheet with id= B, first strand: chain 'A' and resid 1625 through 1627 removed outlier: 3.615A pdb=" N LEU A1625 " --> pdb=" O MET A1615 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1793 through 1796 Processing sheet with id= D, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 7.505A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR A2057 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A1951 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A2059 " --> pdb=" O VAL A1951 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N SER A1953 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE A2061 " --> pdb=" O SER A1953 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A2020 " --> pdb=" O GLU A2060 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1985 " --> pdb=" O HIS A2017 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id= F, first strand: chain 'A' and resid 2266 through 2269 removed outlier: 4.000A pdb=" N PHE A2268 " --> pdb=" O THR A2277 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A2277 " --> pdb=" O PHE A2268 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id= H, first strand: chain 'A' and resid 2377 through 2380 removed outlier: 4.382A pdb=" N VAL A2377 " --> pdb=" O ILE A2481 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2763 through 2767 removed outlier: 7.059A pdb=" N VAL A2799 " --> pdb=" O HIS A2764 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL A2766 " --> pdb=" O VAL A2799 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL A2801 " --> pdb=" O VAL A2766 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 3128 through 3131 removed outlier: 6.457A pdb=" N TYR A3001 " --> pdb=" O GLU A3129 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N HIS A3131 " --> pdb=" O TYR A3001 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A3003 " --> pdb=" O HIS A3131 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A3107 " --> pdb=" O LEU A3002 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL A3004 " --> pdb=" O LEU A3107 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A3109 " --> pdb=" O VAL A3004 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR A3006 " --> pdb=" O VAL A3109 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU A3111 " --> pdb=" O THR A3006 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A3059 " --> pdb=" O ILE A3108 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A3110 " --> pdb=" O VAL A3059 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A3061 " --> pdb=" O ILE A3110 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N GLU A3112 " --> pdb=" O LEU A3061 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU A3026 " --> pdb=" O VAL A3060 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 3086 through 3091 removed outlier: 4.248A pdb=" N LYS A3086 " --> pdb=" O VAL A3101 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 3398 through 3400 removed outlier: 8.155A pdb=" N VAL A3399 " --> pdb=" O PHE A3274 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A3276 " --> pdb=" O VAL A3399 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A3371 " --> pdb=" O VAL A3273 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR A3275 " --> pdb=" O VAL A3371 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A3373 " --> pdb=" O THR A3275 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE A3277 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE A3375 " --> pdb=" O ILE A3277 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR A3279 " --> pdb=" O PHE A3375 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR A3377 " --> pdb=" O THR A3279 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A3304 " --> pdb=" O VAL A3335 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLN A3337 " --> pdb=" O VAL A3304 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU A3306 " --> pdb=" O GLN A3337 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP A3339 " --> pdb=" O LEU A3306 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 4880 through 4883 1485 hydrogen bonds defined for protein. 4335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.84 Time building geometry restraints manager: 14.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 10804 1.34 - 1.49: 9902 1.49 - 1.64: 15321 1.64 - 1.80: 135 1.80 - 1.95: 175 Bond restraints: 36337 Sorted by residual: bond pdb=" C ALA A3411 " pdb=" N SER A3412 " ideal model delta sigma weight residual 1.328 1.289 0.039 1.13e-02 7.83e+03 1.17e+01 bond pdb=" C THR A3415 " pdb=" N LYS A3416 " ideal model delta sigma weight residual 1.335 1.294 0.041 1.30e-02 5.92e+03 9.89e+00 bond pdb=" C LYS A2731 " pdb=" N PRO A2732 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.12e-02 7.97e+03 8.33e+00 bond pdb=" CA ILE A1901 " pdb=" CB ILE A1901 " ideal model delta sigma weight residual 1.534 1.553 -0.018 6.80e-03 2.16e+04 7.28e+00 bond pdb=" N GLN A4701 " pdb=" CA GLN A4701 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.23e-02 6.61e+03 5.74e+00 ... (remaining 36332 not shown) Histogram of bond angle deviations from ideal: 95.48 - 104.34: 573 104.34 - 113.20: 19141 113.20 - 122.07: 22850 122.07 - 130.93: 6378 130.93 - 139.80: 233 Bond angle restraints: 49175 Sorted by residual: angle pdb=" O LEU A1494 " pdb=" C LEU A1494 " pdb=" N SER A1495 " ideal model delta sigma weight residual 122.59 137.07 -14.48 1.33e+00 5.65e-01 1.18e+02 angle pdb=" CA GLN A4701 " pdb=" CB GLN A4701 " pdb=" CG GLN A4701 " ideal model delta sigma weight residual 114.10 132.05 -17.95 2.00e+00 2.50e-01 8.05e+01 angle pdb=" CA LEU A1494 " pdb=" C LEU A1494 " pdb=" N SER A1495 " ideal model delta sigma weight residual 116.84 103.37 13.47 1.71e+00 3.42e-01 6.20e+01 angle pdb=" C PRO A3121 " pdb=" N VAL A3122 " pdb=" CA VAL A3122 " ideal model delta sigma weight residual 122.13 136.42 -14.29 1.85e+00 2.92e-01 5.97e+01 angle pdb=" N GLN A4701 " pdb=" CA GLN A4701 " pdb=" CB GLN A4701 " ideal model delta sigma weight residual 110.16 121.11 -10.95 1.48e+00 4.57e-01 5.47e+01 ... (remaining 49170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.22: 21190 27.22 - 54.43: 804 54.43 - 81.65: 81 81.65 - 108.86: 13 108.86 - 136.08: 3 Dihedral angle restraints: 22091 sinusoidal: 9079 harmonic: 13012 Sorted by residual: dihedral pdb=" CA GLU A1170 " pdb=" C GLU A1170 " pdb=" N ALA A1171 " pdb=" CA ALA A1171 " ideal model delta harmonic sigma weight residual 180.00 133.29 46.71 0 5.00e+00 4.00e-02 8.73e+01 dihedral pdb=" CA GLU A4165 " pdb=" C GLU A4165 " pdb=" N PRO A4166 " pdb=" CA PRO A4166 " ideal model delta harmonic sigma weight residual -180.00 -136.97 -43.03 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CA GLU A1016 " pdb=" C GLU A1016 " pdb=" N PRO A1017 " pdb=" CA PRO A1017 " ideal model delta harmonic sigma weight residual 180.00 144.32 35.68 0 5.00e+00 4.00e-02 5.09e+01 ... (remaining 22088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4885 0.106 - 0.211: 583 0.211 - 0.317: 62 0.317 - 0.422: 14 0.422 - 0.528: 4 Chirality restraints: 5548 Sorted by residual: chirality pdb=" CB ILE A4792 " pdb=" CA ILE A4792 " pdb=" CG1 ILE A4792 " pdb=" CG2 ILE A4792 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA GLU A4700 " pdb=" N GLU A4700 " pdb=" C GLU A4700 " pdb=" CB GLU A4700 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CB VAL A3543 " pdb=" CA VAL A3543 " pdb=" CG1 VAL A3543 " pdb=" CG2 VAL A3543 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 5545 not shown) Planarity restraints: 6274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1031 " 0.039 2.00e-02 2.50e+03 3.97e-02 3.94e+01 pdb=" CG TRP A1031 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 TRP A1031 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP A1031 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1031 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1031 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1031 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1031 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1031 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP A1031 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A5104 " -0.026 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C VAL A5104 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL A5104 " -0.033 2.00e-02 2.50e+03 pdb=" N SER A5105 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A4322 " 0.042 2.00e-02 2.50e+03 3.45e-02 2.38e+01 pdb=" CG TYR A4322 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TYR A4322 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A4322 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A4322 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A4322 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A4322 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A4322 " -0.003 2.00e-02 2.50e+03 ... (remaining 6271 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 372 2.64 - 3.20: 30469 3.20 - 3.77: 55595 3.77 - 4.33: 71909 4.33 - 4.90: 116655 Nonbonded interactions: 275000 Sorted by model distance: nonbonded pdb=" OE1 GLU A1417 " pdb=" OG SER A1496 " model vdw 2.069 2.440 nonbonded pdb=" O GLY A 936 " pdb=" OG1 THR A3238 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLU A3562 " pdb=" OH TYR A4961 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR A1988 " pdb=" OG SER A2457 " model vdw 2.277 2.440 nonbonded pdb=" O THR A2406 " pdb=" OG1 THR A2443 " model vdw 2.278 2.440 ... (remaining 274995 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 group one per residue 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: 3.910 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: 0.040 Extract box with map and model: 11.440 Check model and map are aligned: 0.550 Set scattering table: 0.360 Process input model: 105.400 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.130 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 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 0.078 36337 Z= 0.358 Angle : 1.319 20.633 49175 Z= 0.680 Chirality : 0.071 0.528 5548 Planarity : 0.008 0.109 6274 Dihedral : 13.979 136.076 13613 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.15 % Favored : 91.67 % Rotamer: Outliers : 0.05 % Allowed : 1.23 % Favored : 98.72 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.09 % 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: -3.63 (0.10), residues: 4394 helix: -2.04 (0.08), residues: 2432 sheet: -1.36 (0.32), residues: 237 loop : -2.96 (0.13), residues: 1725 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 392 average time/residue: 0.5120 time to fit residues: 328.7710 Evaluate side-chains 232 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 4.461 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4091 time to fit residues: 6.5235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 374 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 347 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 402 optimal weight: 0.0020 overall best weight: 3.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN A1395 HIS A1478 ASN A1849 GLN A1928 HIS A1991 HIS A2138 GLN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2270 ASN A2360 ASN A2438 GLN ** A2790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2797 GLN ** A3016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3085 GLN A3359 ASN A3400 HIS ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4196 GLN ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4312 GLN A4347 ASN A4413 ASN A4500 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN A4713 HIS ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4873 ASN A4881 GLN A4939 ASN ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4990 ASN A5005 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 36337 Z= 0.294 Angle : 0.755 15.621 49175 Z= 0.386 Chirality : 0.044 0.210 5548 Planarity : 0.005 0.057 6274 Dihedral : 6.485 134.070 4799 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.17 % Favored : 91.78 % Rotamer: Outliers : 1.39 % Allowed : 8.54 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.05 % 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: -1.90 (0.12), residues: 4394 helix: -0.36 (0.10), residues: 2458 sheet: -1.41 (0.31), residues: 255 loop : -2.56 (0.14), residues: 1681 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 235 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 270 average time/residue: 0.4540 time to fit residues: 212.0726 Evaluate side-chains 232 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 4.251 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3627 time to fit residues: 25.3515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 223 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 334 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 403 optimal weight: 5.9990 chunk 435 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 chunk 399 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 GLN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2438 GLN A2785 GLN ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3016 GLN ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4010 GLN ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4342 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN A4836 ASN ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4957 GLN A5077 HIS ** A5146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 36337 Z= 0.300 Angle : 0.728 12.062 49175 Z= 0.370 Chirality : 0.044 0.198 5548 Planarity : 0.005 0.074 6274 Dihedral : 6.172 132.462 4799 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.69 % Favored : 91.26 % Rotamer: Outliers : 1.34 % Allowed : 11.86 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.02 % 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: -1.41 (0.13), residues: 4394 helix: 0.12 (0.10), residues: 2460 sheet: -1.50 (0.32), residues: 251 loop : -2.45 (0.15), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 206 time to evaluate : 4.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 22 residues processed: 249 average time/residue: 0.4690 time to fit residues: 201.1761 Evaluate side-chains 208 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 4.124 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3456 time to fit residues: 20.1744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 398 optimal weight: 5.9990 chunk 303 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 404 optimal weight: 0.9980 chunk 428 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 383 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1090 GLN A1092 GLN A1395 HIS A1478 ASN A1793 ASN A1928 HIS ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3644 HIS ** A3646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4957 GLN A5146 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36337 Z= 0.156 Angle : 0.649 13.316 49175 Z= 0.317 Chirality : 0.042 0.244 5548 Planarity : 0.004 0.078 6274 Dihedral : 5.832 133.768 4799 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.38 % Rotamer: Outliers : 1.34 % Allowed : 12.92 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.94 (0.13), residues: 4394 helix: 0.54 (0.11), residues: 2445 sheet: -1.28 (0.32), residues: 251 loop : -2.28 (0.15), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 218 time to evaluate : 4.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 27 residues processed: 261 average time/residue: 0.4491 time to fit residues: 205.1170 Evaluate side-chains 216 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 4.541 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3712 time to fit residues: 24.9318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 356 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 318 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 365 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 218 optimal weight: 0.7980 chunk 384 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 ASN A1553 ASN A1660 HIS ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2556 GLN ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4696 GLN ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4789 ASN ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36337 Z= 0.212 Angle : 0.660 14.504 49175 Z= 0.324 Chirality : 0.042 0.237 5548 Planarity : 0.004 0.077 6274 Dihedral : 5.744 135.744 4799 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.10 % Favored : 91.85 % Rotamer: Outliers : 1.36 % Allowed : 14.31 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.83 (0.13), residues: 4394 helix: 0.64 (0.11), residues: 2476 sheet: -1.19 (0.33), residues: 241 loop : -2.30 (0.15), residues: 1677 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 17 residues processed: 237 average time/residue: 0.4799 time to fit residues: 201.1280 Evaluate side-chains 201 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 4.053 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3643 time to fit residues: 17.5042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 144 optimal weight: 0.3980 chunk 385 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 428 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1478 ASN ** A1930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 GLN ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4939 ASN ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5096 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 36337 Z= 0.261 Angle : 0.700 16.862 49175 Z= 0.346 Chirality : 0.042 0.292 5548 Planarity : 0.004 0.074 6274 Dihedral : 5.812 138.544 4799 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.47 % Favored : 91.49 % Rotamer: Outliers : 1.18 % Allowed : 15.52 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.85 (0.13), residues: 4394 helix: 0.62 (0.11), residues: 2468 sheet: -1.17 (0.34), residues: 233 loop : -2.30 (0.15), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 195 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 20 residues processed: 237 average time/residue: 0.4914 time to fit residues: 201.1238 Evaluate side-chains 204 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 4.238 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4103 time to fit residues: 20.6336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 413 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 313 optimal weight: 8.9990 chunk 242 optimal weight: 0.3980 chunk 360 optimal weight: 20.0000 chunk 239 optimal weight: 30.0000 chunk 426 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1553 ASN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36337 Z= 0.167 Angle : 0.665 15.181 49175 Z= 0.321 Chirality : 0.042 0.295 5548 Planarity : 0.004 0.073 6274 Dihedral : 5.665 139.205 4799 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.44 % Rotamer: Outliers : 0.91 % Allowed : 16.10 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.65 (0.13), residues: 4394 helix: 0.76 (0.11), residues: 2469 sheet: -1.06 (0.34), residues: 234 loop : -2.17 (0.15), residues: 1691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 208 time to evaluate : 4.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 232 average time/residue: 0.4599 time to fit residues: 184.9573 Evaluate side-chains 211 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 4.034 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3514 time to fit residues: 19.4465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 264 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 335 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 GLN A1553 ASN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36337 Z= 0.184 Angle : 0.678 15.554 49175 Z= 0.327 Chirality : 0.042 0.272 5548 Planarity : 0.004 0.071 6274 Dihedral : 5.626 139.820 4799 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.92 % Favored : 92.03 % Rotamer: Outliers : 0.65 % Allowed : 16.88 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.58 (0.13), residues: 4394 helix: 0.80 (0.11), residues: 2465 sheet: -1.02 (0.34), residues: 234 loop : -2.11 (0.16), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 4.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 212 average time/residue: 0.4872 time to fit residues: 179.4629 Evaluate side-chains 201 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 4.145 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4076 time to fit residues: 16.7780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 388 optimal weight: 4.9990 chunk 409 optimal weight: 1.9990 chunk 373 optimal weight: 8.9990 chunk 397 optimal weight: 4.9990 chunk 408 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 312 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 359 optimal weight: 20.0000 chunk 376 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN A1553 ASN ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2161 HIS ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4590 HIS A4846 ASN A4909 GLN ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36337 Z= 0.155 Angle : 0.682 16.302 49175 Z= 0.327 Chirality : 0.042 0.266 5548 Planarity : 0.004 0.072 6274 Dihedral : 5.541 140.483 4799 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.37 % Favored : 92.58 % Rotamer: Outliers : 0.43 % Allowed : 17.03 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.54 (0.13), residues: 4394 helix: 0.83 (0.11), residues: 2469 sheet: -0.96 (0.34), residues: 240 loop : -2.11 (0.15), residues: 1685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 210 average time/residue: 0.4638 time to fit residues: 170.2351 Evaluate side-chains 192 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 4.175 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5259 time to fit residues: 10.7118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 396 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 420 optimal weight: 10.0000 chunk 256 optimal weight: 0.2980 chunk 199 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 441 optimal weight: 0.9980 chunk 406 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN ** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2635 HIS ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5017 HIS ** A5146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36337 Z= 0.158 Angle : 0.702 18.573 49175 Z= 0.333 Chirality : 0.042 0.260 5548 Planarity : 0.004 0.071 6274 Dihedral : 5.494 140.639 4799 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer: Outliers : 0.13 % Allowed : 17.53 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.49 (0.13), residues: 4394 helix: 0.86 (0.11), residues: 2459 sheet: -0.95 (0.34), residues: 240 loop : -2.05 (0.15), residues: 1695 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 194 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 198 average time/residue: 0.4738 time to fit residues: 165.9250 Evaluate side-chains 191 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 4.210 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3326 time to fit residues: 6.7722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 215 optimal weight: 5.9990 chunk 279 optimal weight: 7.9990 chunk 374 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 324 optimal weight: 0.5980 chunk 51 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 352 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 361 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3041 GLN A3045 ASN ** A3077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3653 ASN ** A3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4312 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4881 GLN ** A4943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.048157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.034763 restraints weight = 271342.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.035937 restraints weight = 157778.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.036666 restraints weight = 108515.367| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36337 Z= 0.148 Angle : 0.698 18.381 49175 Z= 0.329 Chirality : 0.042 0.258 5548 Planarity : 0.004 0.072 6274 Dihedral : 5.411 140.604 4799 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.15 % Favored : 92.81 % Rotamer: Outliers : 0.30 % Allowed : 17.30 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.40 (0.13), residues: 4394 helix: 0.94 (0.11), residues: 2443 sheet: -0.82 (0.33), residues: 256 loop : -2.01 (0.15), residues: 1695 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5973.33 seconds wall clock time: 112 minutes 56.41 seconds (6776.41 seconds total)