Starting phenix.real_space_refine on Wed Mar 20 10:38:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wzr_32912/03_2024/7wzr_32912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wzr_32912/03_2024/7wzr_32912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wzr_32912/03_2024/7wzr_32912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wzr_32912/03_2024/7wzr_32912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wzr_32912/03_2024/7wzr_32912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wzr_32912/03_2024/7wzr_32912.pdb" } resolution = 4.7 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= 0.001 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 16153 2.51 5 N 5442 2.21 5 O 5442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27037 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 10805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2175, 10805 Classifications: {'peptide': 2175} Incomplete info: {'truncation_to_alanine': 2009} Link IDs: {'PTRANS': 62, 'TRANS': 2112} Chain breaks: 30 Unresolved chain link angles: 62 Unresolved non-hydrogen bonds: 7327 Unresolved non-hydrogen angles: 9376 Unresolved non-hydrogen dihedrals: 6133 Unresolved non-hydrogen chiralities: 691 Planarities with less than four sites: {'GLN:plan1': 89, 'ARG:plan': 99, 'TYR:plan': 93, 'ASN:plan1': 135, 'TRP:plan': 30, 'ASP:plan': 120, 'PHE:plan': 110, 'GLU:plan': 120, 'HIS:plan': 42} Unresolved non-hydrogen planarities: 3887 Chain: "E" Number of atoms: 2758 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 2753 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1884 Unresolved non-hydrogen angles: 2413 Unresolved non-hydrogen dihedrals: 1557 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 17, 'PHE:plan': 26, 'GLU:plan': 44, 'ASP:plan': 35} Unresolved non-hydrogen planarities: 989 Conformer: "B" Number of residues, atoms: 554, 2753 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1884 Unresolved non-hydrogen angles: 2413 Unresolved non-hydrogen dihedrals: 1557 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 17, 'PHE:plan': 26, 'GLU:plan': 44, 'ASP:plan': 35} Unresolved non-hydrogen planarities: 989 bond proxies already assigned to first conformer: 2745 Chain: "F" Number of atoms: 10716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2157, 10716 Classifications: {'peptide': 2157} Incomplete info: {'truncation_to_alanine': 1993} Link IDs: {'PTRANS': 59, 'TRANS': 2097} Chain breaks: 35 Unresolved chain link angles: 59 Unresolved non-hydrogen bonds: 7264 Unresolved non-hydrogen angles: 9295 Unresolved non-hydrogen dihedrals: 6073 Unresolved non-hydrogen chiralities: 686 Planarities with less than four sites: {'GLN:plan1': 89, 'ARG:plan': 98, 'TYR:plan': 92, 'ASN:plan1': 134, 'TRP:plan': 29, 'ASP:plan': 123, 'PHE:plan': 109, 'GLU:plan': 119, 'HIS:plan': 42} Unresolved non-hydrogen planarities: 3862 Chain: "D" Number of atoms: 2758 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 2753 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1884 Unresolved non-hydrogen angles: 2413 Unresolved non-hydrogen dihedrals: 1557 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 17, 'PHE:plan': 26, 'GLU:plan': 44, 'ASP:plan': 35} Unresolved non-hydrogen planarities: 989 Conformer: "B" Number of residues, atoms: 554, 2753 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 15, 'TRANS': 538} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1884 Unresolved non-hydrogen angles: 2413 Unresolved non-hydrogen dihedrals: 1557 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 17, 'PHE:plan': 26, 'GLU:plan': 44, 'ASP:plan': 35} Unresolved non-hydrogen planarities: 989 bond proxies already assigned to first conformer: 2745 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG E 228 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG E 228 " occ=0.50 residue: pdb=" N AARG D 228 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG D 228 " occ=0.50 Time building chain proxies: 19.83, per 1000 atoms: 0.73 Number of scatterers: 27037 At special positions: 0 Unit cell: (214.65, 176.85, 170.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 5442 8.00 N 5442 7.00 C 16153 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: 12.77 Conformation dependent library (CDL) restraints added in 8.2 seconds 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10538 Finding SS restraints... Secondary structure from input PDB file: 316 helices and 3 sheets defined 69.0% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'C' and resid 4 through 18 Processing helix chain 'C' and resid 47 through 57 removed outlier: 4.375A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 83 Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.841A pdb=" N ASP C 104 " --> pdb=" O GLN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 139 Processing helix chain 'C' and resid 139 through 165 removed outlier: 4.552A pdb=" N GLN C 145 " --> pdb=" O PRO C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 189 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.727A pdb=" N ASP C 203 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 228 removed outlier: 4.055A pdb=" N ASN C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 removed outlier: 3.960A pdb=" N VAL C 251 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 285 removed outlier: 4.170A pdb=" N LYS C 272 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 276 " --> pdb=" O LYS C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 309 removed outlier: 3.845A pdb=" N ASN C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 319 Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 385 through 399 removed outlier: 3.571A pdb=" N LEU C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 421 removed outlier: 4.102A pdb=" N SER C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 447 removed outlier: 3.637A pdb=" N PHE C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 490 through 495 Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.677A pdb=" N LYS C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 526 Processing helix chain 'C' and resid 530 through 535 removed outlier: 4.105A pdb=" N GLU C 534 " --> pdb=" O PRO C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 554 Processing helix chain 'C' and resid 566 through 578 removed outlier: 4.314A pdb=" N PHE C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET C 578 " --> pdb=" O GLN C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 597 Proline residue: C 593 - end of helix Processing helix chain 'C' and resid 605 through 618 removed outlier: 3.638A pdb=" N GLN C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 638 removed outlier: 3.973A pdb=" N ALA C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 654 removed outlier: 3.658A pdb=" N THR C 645 " --> pdb=" O ASP C 641 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 676 removed outlier: 3.747A pdb=" N ILE C 663 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 697 Processing helix chain 'C' and resid 703 through 715 Processing helix chain 'C' and resid 718 through 724 Processing helix chain 'C' and resid 724 through 729 removed outlier: 4.527A pdb=" N ILE C 729 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 741 No H-bonds generated for 'chain 'C' and resid 739 through 741' Processing helix chain 'C' and resid 742 through 749 Processing helix chain 'C' and resid 754 through 770 removed outlier: 4.640A pdb=" N LEU C 764 " --> pdb=" O LYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 780 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 803 through 810 removed outlier: 3.759A pdb=" N LEU C 807 " --> pdb=" O THR C 804 " (cutoff:3.500A) Proline residue: C 808 - end of helix Processing helix chain 'C' and resid 811 through 820 removed outlier: 3.923A pdb=" N ILE C 816 " --> pdb=" O THR C 812 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR C 817 " --> pdb=" O LEU C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 844 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 853 through 856 removed outlier: 3.945A pdb=" N SER C 856 " --> pdb=" O ARG C 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 853 through 856' Processing helix chain 'C' and resid 870 through 892 removed outlier: 3.964A pdb=" N GLN C 877 " --> pdb=" O GLN C 873 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 878 " --> pdb=" O LYS C 874 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 879 " --> pdb=" O LYS C 875 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU C 881 " --> pdb=" O GLN C 877 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY C 882 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 884 " --> pdb=" O ILE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 916 removed outlier: 3.842A pdb=" N LYS C 903 " --> pdb=" O THR C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 923 Processing helix chain 'C' and resid 925 through 939 Processing helix chain 'C' and resid 942 through 956 removed outlier: 4.147A pdb=" N ARG C 948 " --> pdb=" O TYR C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 976 Processing helix chain 'C' and resid 981 through 999 Processing helix chain 'C' and resid 999 through 1006 removed outlier: 4.205A pdb=" N ILE C1003 " --> pdb=" O LYS C 999 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1017 removed outlier: 3.810A pdb=" N ALA C1013 " --> pdb=" O TYR C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1026 Processing helix chain 'C' and resid 1026 through 1039 Processing helix chain 'C' and resid 1042 through 1052 removed outlier: 3.834A pdb=" N PHE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1076 removed outlier: 3.764A pdb=" N ARG C1071 " --> pdb=" O VAL C1067 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C1076 " --> pdb=" O LYS C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1105 removed outlier: 4.242A pdb=" N LEU C1095 " --> pdb=" O ILE C1091 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP C1100 " --> pdb=" O GLY C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1124 removed outlier: 3.808A pdb=" N CYS C1113 " --> pdb=" O ASP C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1171 removed outlier: 4.071A pdb=" N ILE C1163 " --> pdb=" O VAL C1159 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL C1165 " --> pdb=" O ASN C1161 " (cutoff:3.500A) Proline residue: C1166 - end of helix Processing helix chain 'C' and resid 1173 through 1189 Processing helix chain 'C' and resid 1190 through 1192 No H-bonds generated for 'chain 'C' and resid 1190 through 1192' Processing helix chain 'C' and resid 1193 through 1197 Processing helix chain 'C' and resid 1212 through 1221 removed outlier: 3.783A pdb=" N VAL C1219 " --> pdb=" O LYS C1215 " (cutoff:3.500A) Processing helix chain 'C' and resid 1243 through 1250 Processing helix chain 'C' and resid 1253 through 1262 Processing helix chain 'C' and resid 1262 through 1267 Processing helix chain 'C' and resid 1273 through 1284 Processing helix chain 'C' and resid 1290 through 1295 Processing helix chain 'C' and resid 1296 through 1298 No H-bonds generated for 'chain 'C' and resid 1296 through 1298' Processing helix chain 'C' and resid 1299 through 1304 Processing helix chain 'C' and resid 1312 through 1324 removed outlier: 4.277A pdb=" N ILE C1321 " --> pdb=" O ASN C1317 " (cutoff:3.500A) Processing helix chain 'C' and resid 1325 through 1328 Processing helix chain 'C' and resid 1335 through 1370 removed outlier: 3.612A pdb=" N LYS C1357 " --> pdb=" O PHE C1353 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C1361 " --> pdb=" O LYS C1357 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C1362 " --> pdb=" O LYS C1358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C1365 " --> pdb=" O THR C1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 1376 through 1391 Processing helix chain 'C' and resid 1392 through 1394 No H-bonds generated for 'chain 'C' and resid 1392 through 1394' Processing helix chain 'C' and resid 1395 through 1405 Processing helix chain 'C' and resid 1409 through 1423 removed outlier: 3.516A pdb=" N SER C1413 " --> pdb=" O SER C1409 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C1416 " --> pdb=" O ARG C1412 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU C1417 " --> pdb=" O SER C1413 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN C1423 " --> pdb=" O GLN C1419 " (cutoff:3.500A) Processing helix chain 'C' and resid 1427 through 1446 removed outlier: 3.702A pdb=" N LYS C1436 " --> pdb=" O GLY C1432 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN C1437 " --> pdb=" O GLN C1433 " (cutoff:3.500A) Processing helix chain 'C' and resid 1449 through 1454 Processing helix chain 'C' and resid 1462 through 1470 Processing helix chain 'C' and resid 1471 through 1473 No H-bonds generated for 'chain 'C' and resid 1471 through 1473' Processing helix chain 'C' and resid 1476 through 1489 removed outlier: 4.108A pdb=" N GLY C1487 " --> pdb=" O PHE C1483 " (cutoff:3.500A) Processing helix chain 'C' and resid 1493 through 1506 removed outlier: 3.590A pdb=" N ARG C1498 " --> pdb=" O LYS C1494 " (cutoff:3.500A) Processing helix chain 'C' and resid 1508 through 1516 removed outlier: 4.824A pdb=" N SER C1514 " --> pdb=" O SER C1510 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER C1516 " --> pdb=" O ILE C1512 " (cutoff:3.500A) Processing helix chain 'C' and resid 1533 through 1545 removed outlier: 4.207A pdb=" N ILE C1537 " --> pdb=" O GLU C1533 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU C1540 " --> pdb=" O SER C1536 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C1541 " --> pdb=" O ILE C1537 " (cutoff:3.500A) Processing helix chain 'C' and resid 1549 through 1560 Processing helix chain 'C' and resid 1566 through 1579 removed outlier: 4.244A pdb=" N LEU C1570 " --> pdb=" O ASP C1566 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU C1571 " --> pdb=" O ARG C1567 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN C1572 " --> pdb=" O GLU C1568 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C1579 " --> pdb=" O ILE C1575 " (cutoff:3.500A) Processing helix chain 'C' and resid 1580 through 1585 Processing helix chain 'C' and resid 1586 through 1602 removed outlier: 3.541A pdb=" N THR C1590 " --> pdb=" O ASP C1586 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN C1591 " --> pdb=" O PRO C1587 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS C1592 " --> pdb=" O LEU C1588 " (cutoff:3.500A) Processing helix chain 'C' and resid 1616 through 1636 removed outlier: 4.633A pdb=" N LEU C1620 " --> pdb=" O LYS C1616 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C1624 " --> pdb=" O LEU C1620 " (cutoff:3.500A) Processing helix chain 'C' and resid 1638 through 1653 Processing helix chain 'C' and resid 1654 through 1656 No H-bonds generated for 'chain 'C' and resid 1654 through 1656' Processing helix chain 'C' and resid 1659 through 1671 removed outlier: 3.793A pdb=" N ASN C1663 " --> pdb=" O ASP C1659 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C1670 " --> pdb=" O ILE C1666 " (cutoff:3.500A) Processing helix chain 'C' and resid 1673 through 1678 removed outlier: 3.929A pdb=" N LYS C1677 " --> pdb=" O PHE C1673 " (cutoff:3.500A) Processing helix chain 'C' and resid 1679 through 1684 Processing helix chain 'C' and resid 1685 through 1699 removed outlier: 3.678A pdb=" N LEU C1696 " --> pdb=" O THR C1692 " (cutoff:3.500A) Processing helix chain 'C' and resid 1703 through 1714 removed outlier: 4.076A pdb=" N SER C1707 " --> pdb=" O LEU C1703 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET C1711 " --> pdb=" O SER C1707 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS C1712 " --> pdb=" O GLU C1708 " (cutoff:3.500A) Processing helix chain 'C' and resid 1722 through 1732 removed outlier: 4.024A pdb=" N GLN C1732 " --> pdb=" O ILE C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1735 through 1752 Processing helix chain 'C' and resid 1758 through 1773 removed outlier: 4.176A pdb=" N LEU C1764 " --> pdb=" O ARG C1760 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C1773 " --> pdb=" O GLU C1769 " (cutoff:3.500A) Processing helix chain 'C' and resid 1787 through 1791 removed outlier: 3.747A pdb=" N PHE C1790 " --> pdb=" O GLN C1787 " (cutoff:3.500A) Processing helix chain 'C' and resid 1805 through 1809 Processing helix chain 'C' and resid 1824 through 1835 Processing helix chain 'C' and resid 1849 through 1855 Processing helix chain 'C' and resid 1870 through 1877 Processing helix chain 'C' and resid 1877 through 1891 removed outlier: 4.336A pdb=" N HIS C1884 " --> pdb=" O ASP C1880 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL C1885 " --> pdb=" O ILE C1881 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU C1886 " --> pdb=" O CYS C1882 " (cutoff:3.500A) Processing helix chain 'C' and resid 1897 through 1906 Processing helix chain 'C' and resid 1917 through 1921 Processing helix chain 'C' and resid 1924 through 1933 removed outlier: 3.737A pdb=" N TYR C1930 " --> pdb=" O LEU C1926 " (cutoff:3.500A) Proline residue: C1931 - end of helix Processing helix chain 'C' and resid 1934 through 1950 removed outlier: 3.609A pdb=" N SER C1944 " --> pdb=" O ALA C1940 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER C1947 " --> pdb=" O ASN C1943 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS C1948 " --> pdb=" O SER C1944 " (cutoff:3.500A) Processing helix chain 'C' and resid 1958 through 1975 Proline residue: C1967 - end of helix Processing helix chain 'C' and resid 1982 through 1986 Processing helix chain 'C' and resid 1987 through 2001 removed outlier: 4.366A pdb=" N SER C1991 " --> pdb=" O GLN C1987 " (cutoff:3.500A) Processing helix chain 'C' and resid 2040 through 2045 Processing helix chain 'C' and resid 2083 through 2085 No H-bonds generated for 'chain 'C' and resid 2083 through 2085' Processing helix chain 'C' and resid 2086 through 2101 removed outlier: 4.203A pdb=" N TYR C2090 " --> pdb=" O GLN C2086 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C2098 " --> pdb=" O ALA C2094 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C2099 " --> pdb=" O THR C2095 " (cutoff:3.500A) Processing helix chain 'C' and resid 2137 through 2146 removed outlier: 4.531A pdb=" N TYR C2146 " --> pdb=" O LEU C2142 " (cutoff:3.500A) Processing helix chain 'C' and resid 2154 through 2156 No H-bonds generated for 'chain 'C' and resid 2154 through 2156' Processing helix chain 'C' and resid 2157 through 2162 Processing helix chain 'C' and resid 2163 through 2165 No H-bonds generated for 'chain 'C' and resid 2163 through 2165' Processing helix chain 'C' and resid 2168 through 2181 removed outlier: 3.672A pdb=" N ASP C2179 " --> pdb=" O MET C2175 " (cutoff:3.500A) Processing helix chain 'C' and resid 2186 through 2193 removed outlier: 4.338A pdb=" N LEU C2190 " --> pdb=" O TYR C2186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2196 through 2212 removed outlier: 5.154A pdb=" N THR C2205 " --> pdb=" O ASN C2201 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG C2208 " --> pdb=" O ASN C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2213 through 2215 No H-bonds generated for 'chain 'C' and resid 2213 through 2215' Processing helix chain 'C' and resid 2216 through 2220 removed outlier: 3.759A pdb=" N ILE C2219 " --> pdb=" O VAL C2216 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2271 removed outlier: 4.059A pdb=" N ALA C2271 " --> pdb=" O ASN C2267 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2282 removed outlier: 3.715A pdb=" N PHE C2281 " --> pdb=" O THR C2277 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C2282 " --> pdb=" O GLU C2278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2277 through 2282' Processing helix chain 'C' and resid 2284 through 2290 Processing helix chain 'C' and resid 2297 through 2302 Processing helix chain 'C' and resid 2302 through 2311 Processing helix chain 'C' and resid 2318 through 2331 Processing helix chain 'C' and resid 2340 through 2352 Processing helix chain 'C' and resid 2353 through 2359 removed outlier: 3.640A pdb=" N SER C2358 " --> pdb=" O GLU C2354 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 213 Processing helix chain 'E' and resid 221 through 227 Processing helix chain 'E' and resid 249 through 263 removed outlier: 3.838A pdb=" N LYS E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 287 Processing helix chain 'E' and resid 294 through 310 removed outlier: 4.123A pdb=" N PHE E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 333 removed outlier: 4.200A pdb=" N LEU E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 380 Processing helix chain 'E' and resid 381 through 382 No H-bonds generated for 'chain 'E' and resid 381 through 382' Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.323A pdb=" N MET E 388 " --> pdb=" O GLN E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 414 through 433 Processing helix chain 'E' and resid 437 through 443 removed outlier: 3.508A pdb=" N LEU E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 462 removed outlier: 3.881A pdb=" N ARG E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 507 removed outlier: 3.569A pdb=" N ILE E 504 " --> pdb=" O LEU E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 563 removed outlier: 4.588A pdb=" N GLY E 538 " --> pdb=" O ALA E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 592 removed outlier: 4.335A pdb=" N MET E 589 " --> pdb=" O GLU E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 618 removed outlier: 4.491A pdb=" N ILE E 608 " --> pdb=" O ARG E 604 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR E 613 " --> pdb=" O GLU E 609 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 618 " --> pdb=" O ILE E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 634 Processing helix chain 'E' and resid 635 through 649 removed outlier: 4.078A pdb=" N ILE E 639 " --> pdb=" O GLU E 635 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET E 640 " --> pdb=" O SER E 636 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE E 645 " --> pdb=" O SER E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 668 removed outlier: 3.872A pdb=" N HIS E 663 " --> pdb=" O GLU E 659 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL E 667 " --> pdb=" O HIS E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 682 removed outlier: 3.504A pdb=" N TYR E 681 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 706 removed outlier: 4.848A pdb=" N ASN E 702 " --> pdb=" O LYS E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 726 removed outlier: 3.534A pdb=" N ILE E 724 " --> pdb=" O MET E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 737 Processing helix chain 'E' and resid 738 through 745 Processing helix chain 'F' and resid 4 through 18 Processing helix chain 'F' and resid 46 through 57 removed outlier: 3.941A pdb=" N THR F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.940A pdb=" N MET F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 4.070A pdb=" N PHE F 70 " --> pdb=" O ASN F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.200A pdb=" N ASP F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 150 through 164 Processing helix chain 'F' and resid 171 through 190 Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.704A pdb=" N LEU F 202 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 228 removed outlier: 4.170A pdb=" N ASN F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 253 removed outlier: 4.832A pdb=" N VAL F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 285 Processing helix chain 'F' and resid 294 through 307 Processing helix chain 'F' and resid 311 through 319 removed outlier: 4.130A pdb=" N ASP F 317 " --> pdb=" O LYS F 313 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS F 318 " --> pdb=" O CYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 326 removed outlier: 4.397A pdb=" N ASP F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.952A pdb=" N VAL F 346 " --> pdb=" O ALA F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 398 Processing helix chain 'F' and resid 413 through 421 removed outlier: 3.845A pdb=" N VAL F 417 " --> pdb=" O LEU F 413 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 449 removed outlier: 3.916A pdb=" N THR F 449 " --> pdb=" O THR F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 472 Processing helix chain 'F' and resid 490 through 495 Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 516 through 527 removed outlier: 3.899A pdb=" N LEU F 527 " --> pdb=" O HIS F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.749A pdb=" N ASP F 533 " --> pdb=" O HIS F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 553 removed outlier: 3.597A pdb=" N LEU F 544 " --> pdb=" O LEU F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 579 removed outlier: 3.738A pdb=" N LYS F 571 " --> pdb=" O ASN F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 597 Proline residue: F 593 - end of helix Processing helix chain 'F' and resid 605 through 618 removed outlier: 4.416A pdb=" N ALA F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 638 removed outlier: 3.797A pdb=" N LEU F 627 " --> pdb=" O VAL F 623 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA F 630 " --> pdb=" O ASN F 626 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 654 Processing helix chain 'F' and resid 658 through 675 removed outlier: 3.802A pdb=" N ILE F 663 " --> pdb=" O TYR F 659 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET F 664 " --> pdb=" O SER F 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 699 Processing helix chain 'F' and resid 708 through 715 Processing helix chain 'F' and resid 716 through 718 No H-bonds generated for 'chain 'F' and resid 716 through 718' Processing helix chain 'F' and resid 719 through 724 removed outlier: 4.027A pdb=" N ILE F 723 " --> pdb=" O THR F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 729 removed outlier: 3.540A pdb=" N ILE F 729 " --> pdb=" O GLN F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 751 removed outlier: 3.944A pdb=" N ALA F 745 " --> pdb=" O LEU F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 770 removed outlier: 4.255A pdb=" N ARG F 769 " --> pdb=" O LYS F 765 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 780 removed outlier: 4.535A pdb=" N VAL F 774 " --> pdb=" O GLN F 770 " (cutoff:3.500A) Processing helix chain 'F' and resid 783 through 792 Processing helix chain 'F' and resid 811 through 820 removed outlier: 3.546A pdb=" N GLU F 815 " --> pdb=" O LYS F 811 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE F 816 " --> pdb=" O THR F 812 " (cutoff:3.500A) Processing helix chain 'F' and resid 831 through 844 Processing helix chain 'F' and resid 846 through 852 Processing helix chain 'F' and resid 853 through 858 Processing helix chain 'F' and resid 867 through 892 removed outlier: 4.875A pdb=" N GLN F 873 " --> pdb=" O GLU F 869 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU F 881 " --> pdb=" O GLN F 877 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY F 882 " --> pdb=" O ASP F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 900 through 916 Processing helix chain 'F' and resid 918 through 925 removed outlier: 4.065A pdb=" N ALA F 925 " --> pdb=" O SER F 921 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 939 Processing helix chain 'F' and resid 942 through 956 removed outlier: 4.559A pdb=" N ARG F 948 " --> pdb=" O TYR F 944 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS F 956 " --> pdb=" O LEU F 952 " (cutoff:3.500A) Processing helix chain 'F' and resid 965 through 976 removed outlier: 3.705A pdb=" N LEU F 969 " --> pdb=" O VAL F 965 " (cutoff:3.500A) Processing helix chain 'F' and resid 977 through 980 removed outlier: 3.539A pdb=" N PHE F 980 " --> pdb=" O TRP F 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 977 through 980' Processing helix chain 'F' and resid 981 through 998 Processing helix chain 'F' and resid 999 through 1005 removed outlier: 4.067A pdb=" N ILE F1003 " --> pdb=" O LYS F 999 " (cutoff:3.500A) Processing helix chain 'F' and resid 1008 through 1017 Processing helix chain 'F' and resid 1021 through 1026 Processing helix chain 'F' and resid 1026 through 1040 Processing helix chain 'F' and resid 1041 through 1050 removed outlier: 4.463A pdb=" N ILE F1045 " --> pdb=" O ASP F1041 " (cutoff:3.500A) Processing helix chain 'F' and resid 1051 through 1053 No H-bonds generated for 'chain 'F' and resid 1051 through 1053' Processing helix chain 'F' and resid 1055 through 1076 Processing helix chain 'F' and resid 1092 through 1106 removed outlier: 3.915A pdb=" N GLY F1096 " --> pdb=" O THR F1092 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1123 Processing helix chain 'F' and resid 1148 through 1163 removed outlier: 4.067A pdb=" N ILE F1163 " --> pdb=" O VAL F1159 " (cutoff:3.500A) Processing helix chain 'F' and resid 1163 through 1171 Processing helix chain 'F' and resid 1175 through 1189 removed outlier: 3.567A pdb=" N PHE F1179 " --> pdb=" O SER F1175 " (cutoff:3.500A) Processing helix chain 'F' and resid 1190 through 1192 No H-bonds generated for 'chain 'F' and resid 1190 through 1192' Processing helix chain 'F' and resid 1193 through 1197 Processing helix chain 'F' and resid 1216 through 1222 removed outlier: 4.228A pdb=" N THR F1222 " --> pdb=" O SER F1218 " (cutoff:3.500A) Processing helix chain 'F' and resid 1243 through 1250 Processing helix chain 'F' and resid 1253 through 1262 Processing helix chain 'F' and resid 1262 through 1268 Processing helix chain 'F' and resid 1273 through 1281 removed outlier: 4.068A pdb=" N SER F1281 " --> pdb=" O HIS F1277 " (cutoff:3.500A) Processing helix chain 'F' and resid 1282 through 1284 No H-bonds generated for 'chain 'F' and resid 1282 through 1284' Processing helix chain 'F' and resid 1288 through 1288 No H-bonds generated for 'chain 'F' and resid 1288 through 1288' Processing helix chain 'F' and resid 1289 through 1295 removed outlier: 3.628A pdb=" N PHE F1293 " --> pdb=" O SER F1289 " (cutoff:3.500A) Processing helix chain 'F' and resid 1299 through 1306 removed outlier: 3.949A pdb=" N ALA F1306 " --> pdb=" O ILE F1302 " (cutoff:3.500A) Processing helix chain 'F' and resid 1312 through 1325 removed outlier: 4.445A pdb=" N ILE F1321 " --> pdb=" O ASN F1317 " (cutoff:3.500A) Processing helix chain 'F' and resid 1337 through 1367 Processing helix chain 'F' and resid 1368 through 1370 No H-bonds generated for 'chain 'F' and resid 1368 through 1370' Processing helix chain 'F' and resid 1375 through 1392 Processing helix chain 'F' and resid 1394 through 1402 removed outlier: 4.225A pdb=" N LEU F1400 " --> pdb=" O PRO F1396 " (cutoff:3.500A) Processing helix chain 'F' and resid 1410 through 1424 Processing helix chain 'F' and resid 1427 through 1446 removed outlier: 3.713A pdb=" N ASN F1437 " --> pdb=" O GLN F1433 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN F1439 " --> pdb=" O LEU F1435 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE F1440 " --> pdb=" O LYS F1436 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE F1445 " --> pdb=" O THR F1441 " (cutoff:3.500A) Processing helix chain 'F' and resid 1448 through 1459 removed outlier: 4.204A pdb=" N ASP F1452 " --> pdb=" O ILE F1448 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR F1457 " --> pdb=" O GLY F1453 " (cutoff:3.500A) Processing helix chain 'F' and resid 1462 through 1472 removed outlier: 4.155A pdb=" N TYR F1472 " --> pdb=" O GLU F1468 " (cutoff:3.500A) Processing helix chain 'F' and resid 1476 through 1489 Processing helix chain 'F' and resid 1493 through 1506 Processing helix chain 'F' and resid 1508 through 1516 removed outlier: 5.075A pdb=" N SER F1514 " --> pdb=" O SER F1510 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER F1516 " --> pdb=" O ILE F1512 " (cutoff:3.500A) Processing helix chain 'F' and resid 1531 through 1533 No H-bonds generated for 'chain 'F' and resid 1531 through 1533' Processing helix chain 'F' and resid 1534 through 1546 removed outlier: 3.692A pdb=" N ALA F1541 " --> pdb=" O ILE F1537 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY F1546 " --> pdb=" O ALA F1542 " (cutoff:3.500A) Processing helix chain 'F' and resid 1547 through 1561 Processing helix chain 'F' and resid 1569 through 1579 removed outlier: 3.877A pdb=" N LEU F1579 " --> pdb=" O ILE F1575 " (cutoff:3.500A) Processing helix chain 'F' and resid 1580 through 1585 Processing helix chain 'F' and resid 1588 through 1602 Processing helix chain 'F' and resid 1614 through 1634 removed outlier: 4.000A pdb=" N ASN F1619 " --> pdb=" O LEU F1615 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU F1620 " --> pdb=" O LYS F1616 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F1623 " --> pdb=" O ASN F1619 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F1624 " --> pdb=" O LEU F1620 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR F1628 " --> pdb=" O LEU F1624 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP F1629 " --> pdb=" O HIS F1625 " (cutoff:3.500A) Processing helix chain 'F' and resid 1640 through 1653 removed outlier: 3.520A pdb=" N THR F1647 " --> pdb=" O LYS F1643 " (cutoff:3.500A) Processing helix chain 'F' and resid 1654 through 1657 removed outlier: 4.261A pdb=" N GLY F1657 " --> pdb=" O GLU F1654 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1654 through 1657' Processing helix chain 'F' and resid 1659 through 1678 removed outlier: 3.775A pdb=" N ASN F1663 " --> pdb=" O ASP F1659 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN F1675 " --> pdb=" O LYS F1671 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU F1676 " --> pdb=" O SER F1672 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F1677 " --> pdb=" O PHE F1673 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET F1678 " --> pdb=" O ASP F1674 " (cutoff:3.500A) Processing helix chain 'F' and resid 1679 through 1684 Processing helix chain 'F' and resid 1685 through 1700 removed outlier: 3.685A pdb=" N LEU F1696 " --> pdb=" O THR F1692 " (cutoff:3.500A) Processing helix chain 'F' and resid 1703 through 1717 removed outlier: 3.932A pdb=" N MET F1711 " --> pdb=" O SER F1707 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N HIS F1712 " --> pdb=" O GLU F1708 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F1715 " --> pdb=" O MET F1711 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG F1716 " --> pdb=" O HIS F1712 " (cutoff:3.500A) Processing helix chain 'F' and resid 1722 through 1732 removed outlier: 3.961A pdb=" N GLN F1732 " --> pdb=" O ILE F1728 " (cutoff:3.500A) Processing helix chain 'F' and resid 1735 through 1751 Processing helix chain 'F' and resid 1758 through 1772 removed outlier: 3.635A pdb=" N VAL F1763 " --> pdb=" O ASP F1759 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU F1764 " --> pdb=" O ARG F1760 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP F1770 " --> pdb=" O LYS F1766 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU F1771 " --> pdb=" O PHE F1767 " (cutoff:3.500A) Processing helix chain 'F' and resid 1782 through 1788 Processing helix chain 'F' and resid 1789 through 1791 No H-bonds generated for 'chain 'F' and resid 1789 through 1791' Processing helix chain 'F' and resid 1803 through 1814 removed outlier: 3.654A pdb=" N SER F1808 " --> pdb=" O GLY F1804 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU F1811 " --> pdb=" O TYR F1807 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU F1812 " --> pdb=" O SER F1808 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG F1813 " --> pdb=" O ARG F1809 " (cutoff:3.500A) Processing helix chain 'F' and resid 1824 through 1835 Processing helix chain 'F' and resid 1849 through 1855 Processing helix chain 'F' and resid 1870 through 1891 removed outlier: 4.755A pdb=" N VAL F1885 " --> pdb=" O ILE F1881 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU F1886 " --> pdb=" O CYS F1882 " (cutoff:3.500A) Processing helix chain 'F' and resid 1897 through 1906 Processing helix chain 'F' and resid 1917 through 1935 Proline residue: F1931 - end of helix Processing helix chain 'F' and resid 1939 through 1951 Processing helix chain 'F' and resid 1957 through 1975 Proline residue: F1967 - end of helix Processing helix chain 'F' and resid 1988 through 2001 Processing helix chain 'F' and resid 2040 through 2044 removed outlier: 3.719A pdb=" N VAL F2044 " --> pdb=" O PHE F2040 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2040 through 2044' Processing helix chain 'F' and resid 2083 through 2086 removed outlier: 3.822A pdb=" N GLN F2086 " --> pdb=" O ASP F2083 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2083 through 2086' Processing helix chain 'F' and resid 2087 through 2101 removed outlier: 3.946A pdb=" N GLN F2092 " --> pdb=" O ASN F2088 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE F2093 " --> pdb=" O GLN F2089 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA F2094 " --> pdb=" O TYR F2090 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP F2098 " --> pdb=" O ALA F2094 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE F2099 " --> pdb=" O THR F2095 " (cutoff:3.500A) Processing helix chain 'F' and resid 2137 through 2146 removed outlier: 4.387A pdb=" N TYR F2146 " --> pdb=" O LEU F2142 " (cutoff:3.500A) Processing helix chain 'F' and resid 2154 through 2156 No H-bonds generated for 'chain 'F' and resid 2154 through 2156' Processing helix chain 'F' and resid 2157 through 2162 Processing helix chain 'F' and resid 2166 through 2172 removed outlier: 3.649A pdb=" N GLU F2172 " --> pdb=" O ASP F2168 " (cutoff:3.500A) Processing helix chain 'F' and resid 2173 through 2180 Processing helix chain 'F' and resid 2196 through 2213 removed outlier: 3.779A pdb=" N THR F2205 " --> pdb=" O ASN F2201 " (cutoff:3.500A) Processing helix chain 'F' and resid 2216 through 2221 Processing helix chain 'F' and resid 2265 through 2270 Processing helix chain 'F' and resid 2278 through 2282 Processing helix chain 'F' and resid 2284 through 2289 Processing helix chain 'F' and resid 2297 through 2302 Processing helix chain 'F' and resid 2302 through 2311 Processing helix chain 'F' and resid 2317 through 2329 Processing helix chain 'F' and resid 2340 through 2352 Processing helix chain 'F' and resid 2353 through 2359 Processing helix chain 'D' and resid 201 through 213 Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 249 through 263 removed outlier: 3.530A pdb=" N LYS D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 287 Processing helix chain 'D' and resid 294 through 310 removed outlier: 3.976A pdb=" N PHE D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 333 Processing helix chain 'D' and resid 355 through 381 Processing helix chain 'D' and resid 392 through 407 removed outlier: 3.829A pdb=" N LEU D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 435 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 462 removed outlier: 4.325A pdb=" N ARG D 456 " --> pdb=" O ASP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 487 Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.609A pdb=" N SER D 505 " --> pdb=" O GLY D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 563 Processing helix chain 'D' and resid 572 through 592 removed outlier: 4.266A pdb=" N MET D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 621 removed outlier: 4.258A pdb=" N LEU D 603 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 634 Processing helix chain 'D' and resid 634 through 647 removed outlier: 4.407A pdb=" N LEU D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 639 " --> pdb=" O GLU D 635 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 668 Processing helix chain 'D' and resid 668 through 682 Processing helix chain 'D' and resid 693 through 707 Processing helix chain 'D' and resid 714 through 726 removed outlier: 3.699A pdb=" N ILE D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 737 Processing helix chain 'D' and resid 738 through 746 Processing sheet with id=AA1, first strand: chain 'C' and resid 2066 through 2067 removed outlier: 4.653A pdb=" N ILE C2077 " --> pdb=" O ILE C2067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 2080 through 2081 removed outlier: 3.577A pdb=" N LYS C2080 " --> pdb=" O GLY C2127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 2065 through 2066 removed outlier: 3.863A pdb=" N LEU F2065 " --> pdb=" O CYS F2079 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F2080 " --> pdb=" O GLY F2127 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY F2127 " --> pdb=" O LYS F2080 " (cutoff:3.500A) 2259 hydrogen bonds defined for protein. 6690 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: 12.93 Time building geometry restraints manager: 13.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 5322 1.26 - 1.33: 3996 1.33 - 1.41: 1497 1.41 - 1.49: 5088 1.49 - 1.56: 11065 Bond restraints: 26968 Sorted by residual: bond pdb=" C LEU C 343 " pdb=" O LEU C 343 " ideal model delta sigma weight residual 1.235 1.323 -0.087 1.26e-02 6.30e+03 4.79e+01 bond pdb=" CA SER F 457 " pdb=" C SER F 457 " ideal model delta sigma weight residual 1.523 1.433 0.091 1.34e-02 5.57e+03 4.58e+01 bond pdb=" N PHE C 319 " pdb=" CA PHE C 319 " ideal model delta sigma weight residual 1.462 1.531 -0.069 1.06e-02 8.90e+03 4.22e+01 bond pdb=" C CYS F 267 " pdb=" O CYS F 267 " ideal model delta sigma weight residual 1.234 1.303 -0.069 1.16e-02 7.43e+03 3.53e+01 bond pdb=" C ARG C 353 " pdb=" O ARG C 353 " ideal model delta sigma weight residual 1.236 1.305 -0.069 1.16e-02 7.43e+03 3.50e+01 ... (remaining 26963 not shown) Histogram of bond angle deviations from ideal: 97.61 - 104.60: 172 104.60 - 111.58: 12789 111.58 - 118.57: 8833 118.57 - 125.56: 15680 125.56 - 132.54: 67 Bond angle restraints: 37541 Sorted by residual: angle pdb=" N GLN F1750 " pdb=" CA GLN F1750 " pdb=" C GLN F1750 " ideal model delta sigma weight residual 111.07 97.61 13.46 1.07e+00 8.73e-01 1.58e+02 angle pdb=" N LEU F2336 " pdb=" CA LEU F2336 " pdb=" C LEU F2336 " ideal model delta sigma weight residual 114.56 103.83 10.73 1.27e+00 6.20e-01 7.14e+01 angle pdb=" N GLU F1140 " pdb=" CA GLU F1140 " pdb=" C GLU F1140 " ideal model delta sigma weight residual 112.26 101.42 10.84 1.32e+00 5.74e-01 6.74e+01 angle pdb=" N GLY C2251 " pdb=" CA GLY C2251 " pdb=" C GLY C2251 " ideal model delta sigma weight residual 114.85 103.91 10.94 1.35e+00 5.49e-01 6.57e+01 angle pdb=" N ASP C1736 " pdb=" CA ASP C1736 " pdb=" C ASP C1736 " ideal model delta sigma weight residual 112.23 122.41 -10.18 1.26e+00 6.30e-01 6.53e+01 ... (remaining 37536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.97: 13908 5.97 - 11.95: 1329 11.95 - 17.92: 450 17.92 - 23.89: 156 23.89 - 29.87: 68 Dihedral angle restraints: 15911 sinusoidal: 0 harmonic: 15911 Sorted by residual: dihedral pdb=" CA TYR D 681 " pdb=" C TYR D 681 " pdb=" N TYR D 682 " pdb=" CA TYR D 682 " ideal model delta harmonic sigma weight residual 180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU F 265 " pdb=" C LEU F 265 " pdb=" N VAL F 266 " pdb=" CA VAL F 266 " ideal model delta harmonic sigma weight residual -180.00 -150.28 -29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ARG D 592 " pdb=" C ARG D 592 " pdb=" N TYR D 593 " pdb=" CA TYR D 593 " ideal model delta harmonic sigma weight residual 180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 15908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4245 0.078 - 0.155: 886 0.155 - 0.233: 119 0.233 - 0.311: 15 0.311 - 0.389: 4 Chirality restraints: 5269 Sorted by residual: chirality pdb=" CA HIS C 318 " pdb=" N HIS C 318 " pdb=" C HIS C 318 " pdb=" CB HIS C 318 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA PHE C 319 " pdb=" N PHE C 319 " pdb=" C PHE C 319 " pdb=" CB PHE C 319 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA SER C 685 " pdb=" N SER C 685 " pdb=" C SER C 685 " pdb=" CB SER C 685 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 5266 not shown) Planarity restraints: 5373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 266 " -0.028 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C VAL F 266 " 0.096 2.00e-02 2.50e+03 pdb=" O VAL F 266 " -0.036 2.00e-02 2.50e+03 pdb=" N CYS F 267 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F1674 " -0.023 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C ASP F1674 " 0.082 2.00e-02 2.50e+03 pdb=" O ASP F1674 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN F1675 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F1076 " -0.022 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C ARG F1076 " 0.076 2.00e-02 2.50e+03 pdb=" O ARG F1076 " -0.028 2.00e-02 2.50e+03 pdb=" N SER F1077 " -0.027 2.00e-02 2.50e+03 ... (remaining 5370 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4955 2.75 - 3.28: 31048 3.28 - 3.82: 42465 3.82 - 4.36: 43082 4.36 - 4.90: 64081 Nonbonded interactions: 185631 Sorted by model distance: nonbonded pdb=" O ALA C1576 " pdb=" N LEU C1579 " model vdw 2.208 2.520 nonbonded pdb=" O THR C1395 " pdb=" N ASP C1398 " model vdw 2.220 2.520 nonbonded pdb=" O LYS C2252 " pdb=" N LEU C2254 " model vdw 2.225 2.520 nonbonded pdb=" O GLN C1965 " pdb=" N ASP C1969 " model vdw 2.236 2.520 nonbonded pdb=" O SER C1808 " pdb=" N LEU C1811 " model vdw 2.238 2.520 ... (remaining 185626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 127 or resid 133 through 146 or resid 149 throug \ h 675 or resid 687 through 699 or resid 707 through 1774 or resid 1785 through 1 \ 935 or resid 1938 through 1975 or resid 1984 through 2254 or resid 2265 through \ 2367)) selection = (chain 'F' and (resid 2 through 229 or resid 237 through 749 or resid 753 throug \ h 1774 or resid 1785 through 1792 or resid 1798 through 2254 or resid 2265 throu \ gh 2311 or resid 2317 through 2367)) } ncs_group { reference = (chain 'D' and (resid 189 through 227 or resid 229 through 747)) selection = (chain 'E' and (resid 189 through 227 or resid 229 through 747)) } 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=0.50 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: 1.370 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: 0.020 Extract box with map and model: 5.420 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 87.510 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 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 : 0.008 0.091 26968 Z= 0.584 Angle : 1.209 15.695 37541 Z= 0.851 Chirality : 0.063 0.389 5269 Planarity : 0.005 0.056 5373 Dihedral : 7.949 29.866 5373 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 1.15 % Allowed : 21.63 % Favored : 77.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.06 % 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: -4.58 (0.10), residues: 5304 helix: -2.36 (0.08), residues: 3135 sheet: None (None), residues: 0 loop : -4.07 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.529 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2869 time to fit residues: 69.4980 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 457 optimal weight: 40.0000 chunk 410 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 277 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 258 optimal weight: 30.0000 chunk 316 optimal weight: 20.0000 chunk 492 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26968 Z= 0.223 Angle : 0.669 11.167 37541 Z= 0.404 Chirality : 0.041 0.152 5269 Planarity : 0.004 0.035 5373 Dihedral : 6.592 38.323 5373 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.50 % Favored : 85.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % 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: -3.14 (0.11), residues: 5304 helix: -0.98 (0.08), residues: 3276 sheet: -6.25 (0.67), residues: 10 loop : -3.97 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.913 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2315 time to fit residues: 55.3390 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 273 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 409 optimal weight: 0.9990 chunk 335 optimal weight: 30.0000 chunk 135 optimal weight: 40.0000 chunk 493 optimal weight: 20.0000 chunk 532 optimal weight: 40.0000 chunk 439 optimal weight: 30.0000 chunk 488 optimal weight: 40.0000 chunk 168 optimal weight: 0.0470 chunk 395 optimal weight: 20.0000 overall best weight: 9.6090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26968 Z= 0.302 Angle : 0.770 10.800 37541 Z= 0.473 Chirality : 0.044 0.217 5269 Planarity : 0.005 0.036 5373 Dihedral : 7.333 36.375 5373 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.49 % Allowed : 19.03 % Favored : 80.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.11 % 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: -3.31 (0.11), residues: 5304 helix: -1.16 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -3.98 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.333 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2520 time to fit residues: 59.6656 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 487 optimal weight: 8.9990 chunk 370 optimal weight: 30.0000 chunk 255 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 494 optimal weight: 0.9990 chunk 523 optimal weight: 0.9990 chunk 258 optimal weight: 40.0000 chunk 468 optimal weight: 50.0000 chunk 141 optimal weight: 0.3980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 26968 Z= 0.113 Angle : 0.514 7.394 37541 Z= 0.303 Chirality : 0.038 0.179 5269 Planarity : 0.002 0.032 5373 Dihedral : 5.535 31.651 5373 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.91 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.50 (0.12), residues: 5304 helix: 0.42 (0.09), residues: 3306 sheet: -6.10 (0.51), residues: 30 loop : -3.52 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2274 time to fit residues: 54.8904 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 436 optimal weight: 5.9990 chunk 297 optimal weight: 30.0000 chunk 7 optimal weight: 0.3980 chunk 390 optimal weight: 40.0000 chunk 216 optimal weight: 40.0000 chunk 447 optimal weight: 50.0000 chunk 362 optimal weight: 20.0000 chunk 0 optimal weight: 70.0000 chunk 267 optimal weight: 50.0000 chunk 470 optimal weight: 50.0000 chunk 132 optimal weight: 30.0000 overall best weight: 17.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 26968 Z= 0.481 Angle : 0.953 13.232 37541 Z= 0.597 Chirality : 0.048 0.239 5269 Planarity : 0.006 0.040 5373 Dihedral : 8.269 41.907 5373 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 1.08 % Allowed : 20.84 % Favored : 78.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.23 % 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: -3.85 (0.10), residues: 5304 helix: -1.63 (0.08), residues: 3145 sheet: None (None), residues: 0 loop : -4.01 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.637 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2342 time to fit residues: 56.5151 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 176 optimal weight: 4.9990 chunk 471 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 307 optimal weight: 0.0370 chunk 129 optimal weight: 50.0000 chunk 524 optimal weight: 30.0000 chunk 435 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 43 optimal weight: 40.0000 chunk 173 optimal weight: 8.9990 chunk 275 optimal weight: 50.0000 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26968 Z= 0.187 Angle : 0.605 8.060 37541 Z= 0.364 Chirality : 0.040 0.203 5269 Planarity : 0.003 0.034 5373 Dihedral : 6.535 33.233 5373 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.63 % Favored : 84.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -2.62 (0.11), residues: 5304 helix: -0.51 (0.09), residues: 3240 sheet: -5.83 (1.00), residues: 10 loop : -3.83 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.412 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2329 time to fit residues: 55.9448 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 505 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 298 optimal weight: 0.9980 chunk 382 optimal weight: 7.9990 chunk 296 optimal weight: 40.0000 chunk 441 optimal weight: 5.9990 chunk 292 optimal weight: 9.9990 chunk 522 optimal weight: 20.0000 chunk 326 optimal weight: 0.9990 chunk 318 optimal weight: 2.9990 chunk 241 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26968 Z= 0.136 Angle : 0.523 7.309 37541 Z= 0.313 Chirality : 0.039 0.194 5269 Planarity : 0.002 0.033 5373 Dihedral : 5.654 29.850 5373 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 15.50 % Favored : 84.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.64 (0.12), residues: 5304 helix: 0.37 (0.09), residues: 3276 sheet: -5.71 (1.07), residues: 10 loop : -3.69 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.967 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2328 time to fit residues: 55.4219 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 323 optimal weight: 50.0000 chunk 208 optimal weight: 30.0000 chunk 312 optimal weight: 30.0000 chunk 157 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 332 optimal weight: 20.0000 chunk 355 optimal weight: 30.0000 chunk 258 optimal weight: 40.0000 chunk 48 optimal weight: 9.9990 chunk 410 optimal weight: 40.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 26968 Z= 0.320 Angle : 0.734 9.586 37541 Z= 0.454 Chirality : 0.043 0.202 5269 Planarity : 0.004 0.037 5373 Dihedral : 7.075 33.856 5373 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 20.10 % Favored : 79.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.08 % 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: -2.88 (0.11), residues: 5304 helix: -0.73 (0.09), residues: 3236 sheet: None (None), residues: 0 loop : -3.93 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.900 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2548 time to fit residues: 60.4240 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 475 optimal weight: 50.0000 chunk 500 optimal weight: 10.0000 chunk 456 optimal weight: 30.0000 chunk 486 optimal weight: 40.0000 chunk 293 optimal weight: 30.0000 chunk 212 optimal weight: 0.9980 chunk 382 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 chunk 439 optimal weight: 20.0000 chunk 460 optimal weight: 50.0000 chunk 485 optimal weight: 0.6980 overall best weight: 8.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26968 Z= 0.245 Angle : 0.633 7.823 37541 Z= 0.389 Chirality : 0.041 0.204 5269 Planarity : 0.003 0.035 5373 Dihedral : 6.514 31.194 5373 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 18.14 % Favored : 81.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.06 % 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: -2.57 (0.11), residues: 5304 helix: -0.45 (0.09), residues: 3262 sheet: -5.61 (1.19), residues: 10 loop : -3.89 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.142 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2452 time to fit residues: 58.2789 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 319 optimal weight: 0.9990 chunk 514 optimal weight: 0.9980 chunk 314 optimal weight: 0.0270 chunk 244 optimal weight: 7.9990 chunk 357 optimal weight: 4.9990 chunk 539 optimal weight: 8.9990 chunk 496 optimal weight: 7.9990 chunk 429 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 332 optimal weight: 30.0000 chunk 263 optimal weight: 50.0000 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26968 Z= 0.123 Angle : 0.499 7.314 37541 Z= 0.298 Chirality : 0.039 0.194 5269 Planarity : 0.002 0.033 5373 Dihedral : 5.517 30.055 5373 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.06 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.39 (0.12), residues: 5304 helix: 0.62 (0.09), residues: 3282 sheet: -5.57 (1.20), residues: 10 loop : -3.70 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2453 time to fit residues: 59.0095 Evaluate side-chains 116 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 542 random chunks: chunk 341 optimal weight: 1.9990 chunk 458 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 396 optimal weight: 0.9990 chunk 63 optimal weight: 40.0000 chunk 119 optimal weight: 30.0000 chunk 430 optimal weight: 0.5980 chunk 180 optimal weight: 50.0000 chunk 442 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 79 optimal weight: 50.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.073175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059433 restraints weight = 395667.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.058629 restraints weight = 421816.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058877 restraints weight = 420677.624| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.019 26968 Z= 0.091 Angle : 0.443 7.063 37541 Z= 0.262 Chirality : 0.038 0.184 5269 Planarity : 0.002 0.032 5373 Dihedral : 4.716 28.441 5373 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.31 % Favored : 88.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 5304 helix: 1.70 (0.09), residues: 3342 sheet: -5.49 (1.20), residues: 10 loop : -3.53 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 121 PHE 0.000 0.000 PHE C 70 TYR 0.000 0.000 TYR C 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3563.20 seconds wall clock time: 64 minutes 36.45 seconds (3876.45 seconds total)