Starting phenix.real_space_refine on Mon Sep 14 18:08:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5gap_8014/09_2026/5gap_8014.cif Found real_map, /net/cci-nas-00/data/ceres_data/5gap_8014/09_2026/5gap_8014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5gap_8014/09_2026/5gap_8014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5gap_8014/09_2026/5gap_8014.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5gap_8014/09_2026/5gap_8014.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5gap_8014/09_2026/5gap_8014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5gap_8014/09_2026/5gap_8014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5gap_8014/09_2026/5gap_8014.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 121 5.16 5 C 19527 2.51 5 N 5491 2.21 5 O 6294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31576 Number of models: 1 Model: "" Number of chains: 12 Chain: "V" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1426 Classifications: {'RNAv2': 67} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 56} Chain: "W" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1190 Classifications: {'RNAv2': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 25} Link IDs: {'rna2p': 6, 'rna3p': 49} Chain breaks: 2 Chain: "U" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 17} Chain: "x" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 410 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'UNK:plan-1': 82} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 11066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 11066 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 56, 'TRANS': 1289} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2789 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 348} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 5822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5822 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 700} Chain breaks: 4 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "D" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1151 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "F" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3218 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 15, 'TRANS': 396} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2632 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 115} Chain: "B" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 522 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 65} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 6.08, per 1000 atoms: 0.19 Number of scatterers: 31576 At special positions: 0 Unit cell: (183.04, 155.87, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 143 15.00 O 6294 8.00 N 5491 7.00 C 19527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6876 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 19 sheets defined 59.4% alpha, 9.2% beta 44 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'x' and resid 21 through 46 Processing helix chain 'x' and resid 53 through 62 Processing helix chain 'x' and resid 102 through 120 Processing helix chain 'A' and resid 752 through 770 removed outlier: 4.196A pdb=" N LEU A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 796 removed outlier: 3.664A pdb=" N LYS A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 837 removed outlier: 3.765A pdb=" N SER A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 871 Processing helix chain 'A' and resid 875 through 894 Processing helix chain 'A' and resid 908 through 926 removed outlier: 4.207A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 985 through 1007 removed outlier: 3.665A pdb=" N ILE A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1034 Processing helix chain 'A' and resid 1057 through 1061 Processing helix chain 'A' and resid 1062 through 1074 removed outlier: 3.520A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1087 Processing helix chain 'A' and resid 1109 through 1127 Processing helix chain 'A' and resid 1127 through 1136 Processing helix chain 'A' and resid 1149 through 1156 removed outlier: 3.611A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 Processing helix chain 'A' and resid 1216 through 1234 Processing helix chain 'A' and resid 1273 through 1275 No H-bonds generated for 'chain 'A' and resid 1273 through 1275' Processing helix chain 'A' and resid 1305 through 1321 Processing helix chain 'A' and resid 1327 through 1347 Processing helix chain 'A' and resid 1348 through 1351 Processing helix chain 'A' and resid 1353 through 1376 Processing helix chain 'A' and resid 1385 through 1390 Processing helix chain 'A' and resid 1408 through 1413 removed outlier: 3.553A pdb=" N SER A1413 " --> pdb=" O SER A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1444 removed outlier: 3.924A pdb=" N ILE A1444 " --> pdb=" O PHE A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1471 Processing helix chain 'A' and resid 1490 through 1495 removed outlier: 4.227A pdb=" N LEU A1494 " --> pdb=" O ARG A1490 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A1495 " --> pdb=" O ILE A1491 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1490 through 1495' Processing helix chain 'A' and resid 1498 through 1503 Processing helix chain 'A' and resid 1507 through 1515 Processing helix chain 'A' and resid 1516 through 1518 No H-bonds generated for 'chain 'A' and resid 1516 through 1518' Processing helix chain 'A' and resid 1529 through 1534 Processing helix chain 'A' and resid 1539 through 1550 Processing helix chain 'A' and resid 1551 through 1560 removed outlier: 4.058A pdb=" N THR A1555 " --> pdb=" O GLY A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1566 Processing helix chain 'A' and resid 1577 through 1586 Processing helix chain 'A' and resid 1591 through 1615 Proline residue: A1602 - end of helix Proline residue: A1612 - end of helix Processing helix chain 'A' and resid 1638 through 1649 Processing helix chain 'A' and resid 1652 through 1672 Processing helix chain 'A' and resid 1672 through 1677 removed outlier: 4.096A pdb=" N LEU A1676 " --> pdb=" O GLU A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1693 removed outlier: 4.432A pdb=" N SER A1691 " --> pdb=" O PRO A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1762 removed outlier: 3.709A pdb=" N THR A1761 " --> pdb=" O LEU A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1809 removed outlier: 3.787A pdb=" N LEU A1797 " --> pdb=" O GLY A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1824 Processing helix chain 'A' and resid 1840 through 1845 removed outlier: 3.600A pdb=" N ASN A1845 " --> pdb=" O GLU A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1904 through 1924 Processing helix chain 'A' and resid 1937 through 1939 No H-bonds generated for 'chain 'A' and resid 1937 through 1939' Processing helix chain 'A' and resid 1940 through 1948 Processing helix chain 'A' and resid 1963 through 1969 removed outlier: 4.200A pdb=" N SER A1966 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A1969 " --> pdb=" O SER A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1981 Processing helix chain 'A' and resid 1994 through 1998 Processing helix chain 'A' and resid 2000 through 2018 Processing helix chain 'A' and resid 2018 through 2027 Processing helix chain 'A' and resid 2044 through 2068 Processing helix chain 'A' and resid 2074 through 2084 Processing helix chain 'A' and resid 2092 through 2104 Processing helix chain 'H' and resid 114 through 145 removed outlier: 3.890A pdb=" N PHE H 123 " --> pdb=" O PHE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 removed outlier: 3.916A pdb=" N GLU H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU H 152 " --> pdb=" O THR H 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 170 Processing helix chain 'J' and resid 171 through 177 Processing helix chain 'J' and resid 186 through 198 Proline residue: J 194 - end of helix Processing helix chain 'J' and resid 206 through 210 Processing helix chain 'J' and resid 219 through 236 removed outlier: 3.689A pdb=" N LYS J 225 " --> pdb=" O GLU J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 255 removed outlier: 4.319A pdb=" N ARG J 255 " --> pdb=" O GLU J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 271 removed outlier: 3.645A pdb=" N ASN J 266 " --> pdb=" O LYS J 262 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU J 270 " --> pdb=" O ASN J 266 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N CYS J 271 " --> pdb=" O GLY J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 285 removed outlier: 3.641A pdb=" N TRP J 278 " --> pdb=" O SER J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 303 removed outlier: 3.523A pdb=" N ASN J 301 " --> pdb=" O ALA J 297 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE J 302 " --> pdb=" O THR J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 317 removed outlier: 4.195A pdb=" N TRP J 310 " --> pdb=" O SER J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 334 Processing helix chain 'J' and resid 337 through 348 removed outlier: 4.098A pdb=" N GLU J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 365 Processing helix chain 'J' and resid 368 through 380 removed outlier: 3.763A pdb=" N GLN J 379 " --> pdb=" O TYR J 375 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER J 380 " --> pdb=" O THR J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 395 removed outlier: 3.520A pdb=" N ILE J 394 " --> pdb=" O SER J 390 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 395 " --> pdb=" O PHE J 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 410 removed outlier: 4.082A pdb=" N SER J 405 " --> pdb=" O ILE J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 435 removed outlier: 3.650A pdb=" N LYS J 426 " --> pdb=" O VAL J 422 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU J 432 " --> pdb=" O GLY J 428 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER J 433 " --> pdb=" O LEU J 429 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN J 435 " --> pdb=" O GLU J 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 454 removed outlier: 3.666A pdb=" N LYS J 446 " --> pdb=" O SER J 442 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU J 451 " --> pdb=" O ARG J 447 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA J 454 " --> pdb=" O ALA J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 476 removed outlier: 3.589A pdb=" N ALA J 463 " --> pdb=" O LEU J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 479 through 491 removed outlier: 3.698A pdb=" N ASN J 483 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 509 Processing helix chain 'J' and resid 511 through 526 Processing helix chain 'J' and resid 531 through 543 removed outlier: 3.947A pdb=" N THR J 543 " --> pdb=" O LEU J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 557 Processing helix chain 'J' and resid 559 through 572 Processing helix chain 'J' and resid 576 through 589 Processing helix chain 'J' and resid 594 through 608 removed outlier: 4.317A pdb=" N PHE J 598 " --> pdb=" O LEU J 594 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE J 599 " --> pdb=" O ASP J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 609 through 624 removed outlier: 3.653A pdb=" N SER J 623 " --> pdb=" O GLN J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 625 through 627 No H-bonds generated for 'chain 'J' and resid 625 through 627' Processing helix chain 'J' and resid 633 through 649 removed outlier: 3.681A pdb=" N TYR J 637 " --> pdb=" O GLU J 633 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR J 639 " --> pdb=" O LEU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 652 through 664 removed outlier: 4.380A pdb=" N LEU J 656 " --> pdb=" O ALA J 652 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 661 " --> pdb=" O ASN J 657 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS J 662 " --> pdb=" O GLU J 658 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE J 664 " --> pdb=" O CYS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 667 through 681 removed outlier: 3.846A pdb=" N PHE J 671 " --> pdb=" O CYS J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 683 through 698 Processing helix chain 'J' and resid 701 through 715 removed outlier: 3.731A pdb=" N TRP J 705 " --> pdb=" O CYS J 701 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 733 removed outlier: 3.831A pdb=" N ALA J 722 " --> pdb=" O ASN J 718 " (cutoff:3.500A) Processing helix chain 'J' and resid 737 through 750 Processing helix chain 'J' and resid 753 through 767 Processing helix chain 'J' and resid 770 through 784 removed outlier: 4.133A pdb=" N GLY J 784 " --> pdb=" O LEU J 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 802 Processing helix chain 'J' and resid 804 through 819 Processing helix chain 'J' and resid 820 through 835 Processing helix chain 'J' and resid 839 through 852 removed outlier: 3.689A pdb=" N VAL J 843 " --> pdb=" O GLY J 839 " (cutoff:3.500A) Processing helix chain 'J' and resid 856 through 863 Processing helix chain 'J' and resid 871 through 880 Processing helix chain 'J' and resid 889 through 898 Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.706A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 53 removed outlier: 3.713A pdb=" N GLU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 127 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.592A pdb=" N LEU F 57 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA F 58 " --> pdb=" O PHE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 78 Proline residue: F 75 - end of helix Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 96 through 121 Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 125 through 131 removed outlier: 4.416A pdb=" N SER F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 146 Processing helix chain 'F' and resid 155 through 164 removed outlier: 3.505A pdb=" N HIS F 160 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 161 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 190 through 226 removed outlier: 4.494A pdb=" N SER F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 234 through 246 Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 255 through 260 removed outlier: 3.508A pdb=" N ILE F 259 " --> pdb=" O PRO F 255 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA F 260 " --> pdb=" O SER F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 260' Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.878A pdb=" N PHE F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 293 Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'F' and resid 328 through 346 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.548A pdb=" N LYS F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 389 Processing helix chain 'F' and resid 410 through 414 removed outlier: 3.772A pdb=" N SER F 413 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN F 414 " --> pdb=" O GLY F 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 410 through 414' Processing helix chain 'F' and resid 415 through 422 Processing helix chain 'F' and resid 438 through 457 Processing helix chain 'G' and resid 151 through 164 removed outlier: 3.697A pdb=" N HIS G 164 " --> pdb=" O TYR G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 189 removed outlier: 3.944A pdb=" N MET G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 200 removed outlier: 4.337A pdb=" N GLU G 198 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 262 Processing helix chain 'G' and resid 289 through 330 removed outlier: 3.612A pdb=" N GLU G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 363 removed outlier: 3.846A pdb=" N ARG G 353 " --> pdb=" O ASN G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 398 Processing helix chain 'G' and resid 447 through 456 Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'K' and resid 13 through 30 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 65 through 75 removed outlier: 4.240A pdb=" N LEU K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 92 Processing helix chain 'K' and resid 110 through 126 removed outlier: 4.020A pdb=" N ILE K 126 " --> pdb=" O GLU K 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 412 through 423 removed outlier: 4.191A pdb=" N THR B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Proline residue: B 421 - end of helix Processing helix chain 'B' and resid 425 through 433 Processing sheet with id=AA1, first strand: chain 'A' and resid 981 through 983 removed outlier: 6.293A pdb=" N VAL A 967 " --> pdb=" O ASN A1091 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1013 through 1014 removed outlier: 5.752A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A1249 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1258 through 1262 Processing sheet with id=AA4, first strand: chain 'A' and resid 1414 through 1417 Processing sheet with id=AA5, first strand: chain 'A' and resid 1825 through 1827 Processing sheet with id=AA6, first strand: chain 'A' and resid 1678 through 1683 removed outlier: 6.776A pdb=" N GLU A1704 " --> pdb=" O GLU A1679 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A1681 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR A1702 " --> pdb=" O VAL A1681 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N ILE A1701 " --> pdb=" O GLN A1737 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N GLN A1737 " --> pdb=" O ILE A1701 " (cutoff:3.500A) removed outlier: 12.291A pdb=" N MET A1703 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N ASP A1735 " --> pdb=" O MET A1703 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N SER A1705 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N TRP A1733 " --> pdb=" O SER A1705 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N HIS A1707 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS A1731 " --> pdb=" O HIS A1707 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL A1773 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP A1733 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE A1775 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASP A1735 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A1777 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN A1737 " --> pdb=" O ILE A1777 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1955 through 1957 removed outlier: 6.029A pdb=" N LEU A1850 " --> pdb=" O ILE A1934 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A1881 " --> pdb=" O PHE A1890 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 166 through 172 removed outlier: 5.419A pdb=" N LEU H 167 " --> pdb=" O ASN H 465 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN H 465 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY H 169 " --> pdb=" O LEU H 463 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER H 460 " --> pdb=" O GLY H 456 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY H 456 " --> pdb=" O SER H 460 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 452 " --> pdb=" O TRP H 464 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 180 through 183 removed outlier: 3.622A pdb=" N GLN H 200 " --> pdb=" O THR H 192 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL H 201 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN H 208 " --> pdb=" O ASN H 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 221 through 225 removed outlier: 4.180A pdb=" N ALA H 223 " --> pdb=" O CYS H 237 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 243 " --> pdb=" O ASP H 260 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP H 260 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN H 245 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 268 through 273 Processing sheet with id=AB3, first strand: chain 'H' and resid 310 through 315 removed outlier: 3.569A pdb=" N SER H 340 " --> pdb=" O ASP H 335 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 354 through 357 removed outlier: 3.937A pdb=" N VAL H 375 " --> pdb=" O ASN H 387 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN H 387 " --> pdb=" O VAL H 375 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 396 through 400 removed outlier: 4.138A pdb=" N GLY H 414 " --> pdb=" O LEU H 418 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU H 418 " --> pdb=" O GLY H 414 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 419 " --> pdb=" O SER H 432 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER H 432 " --> pdb=" O ILE H 419 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL H 421 " --> pdb=" O MET H 430 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 8 through 9 Processing sheet with id=AB7, first strand: chain 'G' and resid 366 through 371 Processing sheet with id=AB8, first strand: chain 'G' and resid 366 through 371 removed outlier: 3.907A pdb=" N TYR G 337 " --> pdb=" O LEU G 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 406 through 408 Processing sheet with id=AC1, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.395A pdb=" N ALA K 100 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE K 52 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE K 102 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N VAL K 79 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE K 52 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL K 81 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET K 54 " --> pdb=" O VAL K 81 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 9.54 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4941 1.31 - 1.44: 9190 1.44 - 1.56: 17864 1.56 - 1.69: 301 1.69 - 1.82: 208 Bond restraints: 32504 Sorted by residual: bond pdb=" CA ASN A1369 " pdb=" C ASN A1369 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.30e-02 5.92e+03 2.75e+01 bond pdb=" C ASN A1369 " pdb=" O ASN A1369 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.28e+01 bond pdb=" CA ASP D 78 " pdb=" CB ASP D 78 " ideal model delta sigma weight residual 1.522 1.554 -0.032 7.00e-03 2.04e+04 2.08e+01 bond pdb=" N ILE F 222 " pdb=" CA ILE F 222 " ideal model delta sigma weight residual 1.461 1.508 -0.048 1.24e-02 6.50e+03 1.47e+01 bond pdb=" N ILE A 882 " pdb=" CA ILE A 882 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.23e-02 6.61e+03 1.46e+01 ... (remaining 32499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 42642 3.08 - 6.15: 1879 6.15 - 9.23: 121 9.23 - 12.31: 14 12.31 - 15.39: 3 Bond angle restraints: 44659 Sorted by residual: angle pdb=" N THR J 239 " pdb=" CA THR J 239 " pdb=" C THR J 239 " ideal model delta sigma weight residual 111.71 120.62 -8.91 1.15e+00 7.56e-01 6.00e+01 angle pdb=" CA ASN A1369 " pdb=" C ASN A1369 " pdb=" O ASN A1369 " ideal model delta sigma weight residual 120.55 112.66 7.89 1.06e+00 8.90e-01 5.55e+01 angle pdb=" C ILE J 355 " pdb=" CA ILE J 355 " pdb=" CB ILE J 355 " ideal model delta sigma weight residual 111.97 102.89 9.08 1.28e+00 6.10e-01 5.03e+01 angle pdb=" C SER A 979 " pdb=" N PRO A 980 " pdb=" CD PRO A 980 " ideal model delta sigma weight residual 120.60 105.32 15.28 2.20e+00 2.07e-01 4.82e+01 angle pdb=" N LEU K 125 " pdb=" CA LEU K 125 " pdb=" C LEU K 125 " ideal model delta sigma weight residual 110.97 118.00 -7.03 1.09e+00 8.42e-01 4.16e+01 ... (remaining 44654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 18621 35.72 - 71.45: 777 71.45 - 107.17: 34 107.17 - 142.90: 2 142.90 - 178.62: 8 Dihedral angle restraints: 19442 sinusoidal: 8890 harmonic: 10552 Sorted by residual: dihedral pdb=" C4' A V 24 " pdb=" C3' A V 24 " pdb=" C2' A V 24 " pdb=" C1' A V 24 " ideal model delta sinusoidal sigma weight residual 36.35 -38.83 75.18 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' U U 96 " pdb=" C3' U U 96 " pdb=" C2' U U 96 " pdb=" C1' U U 96 " ideal model delta sinusoidal sigma weight residual 36.35 -37.88 74.22 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4' G V 30 " pdb=" C3' G V 30 " pdb=" C2' G V 30 " pdb=" C1' G V 30 " ideal model delta sinusoidal sigma weight residual 36.35 -37.63 73.98 1 3.10e+00 1.04e-01 7.23e+02 ... (remaining 19439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4088 0.114 - 0.228: 851 0.228 - 0.342: 171 0.342 - 0.455: 19 0.455 - 0.569: 7 Chirality restraints: 5136 Sorted by residual: chirality pdb=" CA LYS J 193 " pdb=" N LYS J 193 " pdb=" C LYS J 193 " pdb=" CB LYS J 193 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" CA PHE J 617 " pdb=" N PHE J 617 " pdb=" C PHE J 617 " pdb=" CB PHE J 617 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA PHE J 541 " pdb=" N PHE J 541 " pdb=" C PHE J 541 " pdb=" CB PHE J 541 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 5133 not shown) Planarity restraints: 5181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 979 " 0.091 5.00e-02 4.00e+02 1.41e-01 3.17e+01 pdb=" N PRO A 980 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO A 980 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 980 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G V 44 " 0.078 2.00e-02 2.50e+03 3.17e-02 3.01e+01 pdb=" N9 G V 44 " -0.068 2.00e-02 2.50e+03 pdb=" C8 G V 44 " -0.015 2.00e-02 2.50e+03 pdb=" N7 G V 44 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G V 44 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G V 44 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G V 44 " 0.023 2.00e-02 2.50e+03 pdb=" N1 G V 44 " 0.010 2.00e-02 2.50e+03 pdb=" C2 G V 44 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G V 44 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G V 44 " -0.015 2.00e-02 2.50e+03 pdb=" C4 G V 44 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G V 14 " 0.005 2.00e-02 2.50e+03 2.86e-02 2.45e+01 pdb=" N9 G V 14 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G V 14 " -0.007 2.00e-02 2.50e+03 pdb=" N7 G V 14 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G V 14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G V 14 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G V 14 " 0.046 2.00e-02 2.50e+03 pdb=" N1 G V 14 " -0.079 2.00e-02 2.50e+03 pdb=" C2 G V 14 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G V 14 " 0.037 2.00e-02 2.50e+03 pdb=" N3 G V 14 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G V 14 " 0.000 2.00e-02 2.50e+03 ... (remaining 5178 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 757 2.69 - 3.25: 33406 3.25 - 3.80: 53173 3.80 - 4.35: 69491 4.35 - 4.90: 107447 Nonbonded interactions: 264274 Sorted by model distance: nonbonded pdb=" O ASP J 199 " pdb=" N LEU J 201 " model vdw 2.143 3.120 nonbonded pdb=" O ALA K 40 " pdb=" OG1 THR K 43 " model vdw 2.207 3.040 nonbonded pdb=" O2' A W 49 " pdb=" OP2 G W 50 " model vdw 2.225 3.040 nonbonded pdb=" OP2 A V 18 " pdb=" NZ LYS F 378 " model vdw 2.240 3.120 nonbonded pdb=" O PHE A1562 " pdb=" OG1 THR A1565 " model vdw 2.255 3.040 ... (remaining 264269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.680 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4818 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 0.071 32504 Z= 0.535 Angle : 1.527 15.387 44659 Z= 1.065 Chirality : 0.100 0.569 5136 Planarity : 0.007 0.141 5181 Dihedral : 17.846 178.621 12566 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 1.47 % Allowed : 8.81 % Favored : 89.73 % Rotamer: Outliers : 4.23 % Allowed : 8.96 % Favored : 86.81 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.09 % Twisted Proline : 1.46 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 3475 helix: 1.00 (0.09), residues: 1799 sheet: -2.60 (0.23), residues: 371 loop : -2.79 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 780 TYR 0.042 0.003 TYR J 564 PHE 0.052 0.003 PHE J 617 TRP 0.033 0.003 TRP A 823 HIS 0.009 0.002 HIS G 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.54 (32504) covalent geometry : angle 1.52720 / 1.07 (44659) hydrogen bonds : bond 0.15115 / 7.93 ( 1667) hydrogen bonds : angle 5.62469 / 2.28 ( 4772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 948 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 TYR cc_start: 0.4889 (OUTLIER) cc_final: 0.4528 (t80) REVERT: A 770 MET cc_start: 0.6032 (mtt) cc_final: 0.5320 (mtt) REVERT: A 778 LYS cc_start: 0.4636 (mmmt) cc_final: 0.4184 (tppt) REVERT: A 814 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7351 (tpt170) REVERT: A 839 HIS cc_start: 0.6921 (t70) cc_final: 0.6320 (m-70) REVERT: A 868 GLN cc_start: 0.7009 (tp40) cc_final: 0.6668 (tt0) REVERT: A 1046 SER cc_start: 0.5614 (m) cc_final: 0.5270 (p) REVERT: A 1107 LEU cc_start: 0.5572 (mt) cc_final: 0.5259 (mt) REVERT: A 1151 GLU cc_start: 0.6609 (mp0) cc_final: 0.6409 (tm-30) REVERT: A 1166 ASP cc_start: 0.6308 (m-30) cc_final: 0.6053 (m-30) REVERT: A 1168 ILE cc_start: 0.5819 (pt) cc_final: 0.5541 (pt) REVERT: A 1186 TYR cc_start: 0.5540 (t80) cc_final: 0.4739 (t80) REVERT: A 1190 ASN cc_start: 0.6291 (m110) cc_final: 0.5676 (m-40) REVERT: A 1211 SER cc_start: 0.7919 (m) cc_final: 0.7589 (m) REVERT: A 1214 ARG cc_start: 0.6084 (mtt180) cc_final: 0.4894 (mmt180) REVERT: A 1218 GLN cc_start: 0.5694 (tt0) cc_final: 0.5351 (tm-30) REVERT: A 1240 SER cc_start: 0.5955 (t) cc_final: 0.5709 (p) REVERT: A 1253 LYS cc_start: 0.6800 (pttt) cc_final: 0.6504 (tttm) REVERT: A 1266 GLU cc_start: 0.5117 (mm-30) cc_final: 0.4832 (tp30) REVERT: A 1291 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6269 (tp30) REVERT: A 1348 GLU cc_start: 0.6688 (tt0) cc_final: 0.6468 (tp30) REVERT: A 1404 HIS cc_start: 0.7250 (t70) cc_final: 0.7007 (t70) REVERT: A 1413 SER cc_start: 0.7330 (m) cc_final: 0.6960 (p) REVERT: A 1426 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6497 (mtm110) REVERT: A 1458 TRP cc_start: 0.5251 (m100) cc_final: 0.5042 (m100) REVERT: A 1517 TYR cc_start: 0.6262 (m-80) cc_final: 0.5936 (m-80) REVERT: A 1585 MET cc_start: 0.5099 (tpt) cc_final: 0.4873 (tpp) REVERT: A 1586 GLN cc_start: 0.5610 (tt0) cc_final: 0.5387 (tt0) REVERT: A 1684 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5259 (tm-30) REVERT: A 1719 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6724 (tt0) REVERT: A 1721 ASN cc_start: 0.7244 (t0) cc_final: 0.7007 (p0) REVERT: A 1724 PHE cc_start: 0.5371 (m-80) cc_final: 0.4920 (m-80) REVERT: A 1731 LYS cc_start: 0.6378 (ttpt) cc_final: 0.6173 (ttpp) REVERT: A 1733 TRP cc_start: 0.6229 (p-90) cc_final: 0.5423 (p-90) REVERT: A 1747 ASP cc_start: 0.6268 (t0) cc_final: 0.5972 (t0) REVERT: A 1843 LEU cc_start: 0.7129 (mt) cc_final: 0.6859 (mt) REVERT: A 1885 LYS cc_start: 0.6774 (tptt) cc_final: 0.6288 (mmtp) REVERT: A 1915 GLU cc_start: 0.7720 (tt0) cc_final: 0.7306 (tm-30) REVERT: A 1926 LYS cc_start: 0.6250 (mmmt) cc_final: 0.6040 (mmtt) REVERT: A 1928 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6745 (tp30) REVERT: A 1947 HIS cc_start: 0.5183 (m-70) cc_final: 0.4955 (m170) REVERT: A 1948 MET cc_start: 0.6853 (mmm) cc_final: 0.6595 (mmm) REVERT: A 1950 ASP cc_start: 0.7720 (m-30) cc_final: 0.7307 (t0) REVERT: A 1951 PHE cc_start: 0.6775 (m-80) cc_final: 0.6315 (m-80) REVERT: A 1998 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7554 (mmm160) REVERT: A 2055 MET cc_start: 0.6660 (mmt) cc_final: 0.6450 (mmt) REVERT: A 2078 GLU cc_start: 0.6392 (tm-30) cc_final: 0.6142 (tm-30) REVERT: H 127 TYR cc_start: 0.6376 (t80) cc_final: 0.5915 (t80) REVERT: H 139 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7406 (tt0) REVERT: H 158 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6703 (pt0) REVERT: H 172 LEU cc_start: 0.6317 (pp) cc_final: 0.5770 (pp) REVERT: H 234 MET cc_start: 0.6043 (ptm) cc_final: 0.5776 (ppp) REVERT: H 274 HIS cc_start: 0.7097 (t-90) cc_final: 0.6817 (t-90) REVERT: H 280 ILE cc_start: 0.6329 (mt) cc_final: 0.5967 (mp) REVERT: H 331 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8398 (p) REVERT: H 334 TRP cc_start: 0.7250 (m100) cc_final: 0.6974 (m100) REVERT: H 335 ASP cc_start: 0.7443 (m-30) cc_final: 0.7115 (p0) REVERT: H 372 ILE cc_start: 0.5792 (mt) cc_final: 0.5586 (mt) REVERT: H 388 GLN cc_start: 0.6866 (mt0) cc_final: 0.6614 (mt0) REVERT: J 163 THR cc_start: 0.7637 (p) cc_final: 0.7410 (p) REVERT: J 182 THR cc_start: 0.5374 (p) cc_final: 0.4937 (p) REVERT: J 266 ASN cc_start: 0.6387 (m-40) cc_final: 0.6053 (t0) REVERT: J 290 HIS cc_start: 0.6996 (p-80) cc_final: 0.6575 (t70) REVERT: J 328 ARG cc_start: 0.7837 (ptp90) cc_final: 0.7415 (mtp85) REVERT: J 369 MET cc_start: 0.7075 (ttt) cc_final: 0.6566 (mmm) REVERT: J 492 MET cc_start: 0.5974 (ttm) cc_final: 0.5297 (mmt) REVERT: J 513 THR cc_start: 0.7121 (p) cc_final: 0.6896 (t) REVERT: J 550 ARG cc_start: 0.6284 (ptp-170) cc_final: 0.6045 (ptt-90) REVERT: J 565 VAL cc_start: 0.7544 (t) cc_final: 0.6608 (t) REVERT: J 569 TRP cc_start: 0.6720 (m100) cc_final: 0.6249 (m-10) REVERT: J 578 GLN cc_start: 0.6372 (pt0) cc_final: 0.5631 (mp10) REVERT: J 591 PRO cc_start: 0.4074 (Cg_exo) cc_final: 0.3432 (Cg_endo) REVERT: J 603 LEU cc_start: 0.8139 (mt) cc_final: 0.7821 (mm) REVERT: J 785 ASN cc_start: 0.6288 (m-40) cc_final: 0.5834 (t0) REVERT: J 799 ARG cc_start: 0.7418 (mtt180) cc_final: 0.7213 (mtm110) REVERT: J 809 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6129 (tm) REVERT: J 810 GLU cc_start: 0.5810 (tp30) cc_final: 0.5488 (tp30) REVERT: J 873 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6545 (tp30) REVERT: J 874 TRP cc_start: 0.6516 (OUTLIER) cc_final: 0.6030 (t-100) REVERT: D 17 GLN cc_start: 0.6348 (mm-40) cc_final: 0.6043 (tm-30) REVERT: D 22 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5574 (mm-30) REVERT: D 36 ASP cc_start: 0.5889 (t70) cc_final: 0.5631 (t70) REVERT: D 51 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7651 (pt0) REVERT: D 63 ASP cc_start: 0.5634 (t0) cc_final: 0.5195 (t70) REVERT: D 99 ASN cc_start: 0.4877 (t0) cc_final: 0.4628 (t0) REVERT: F 47 LEU cc_start: 0.5734 (pp) cc_final: 0.5509 (pp) REVERT: F 100 GLU cc_start: 0.7750 (tp30) cc_final: 0.7458 (mt-10) REVERT: F 120 TYR cc_start: 0.5991 (OUTLIER) cc_final: 0.4598 (t80) REVERT: F 144 LEU cc_start: 0.7635 (tp) cc_final: 0.7399 (mt) REVERT: F 145 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6535 (pt0) REVERT: F 201 ASN cc_start: 0.6205 (t0) cc_final: 0.5905 (m110) REVERT: F 271 GLU cc_start: 0.6162 (tt0) cc_final: 0.5900 (pt0) REVERT: F 381 LEU cc_start: 0.7208 (mt) cc_final: 0.6962 (mt) REVERT: F 397 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6849 (pt0) REVERT: F 398 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.5516 (tt0) REVERT: F 412 MET cc_start: 0.5189 (ttm) cc_final: 0.4699 (ttp) REVERT: F 419 GLN cc_start: 0.5720 (OUTLIER) cc_final: 0.5174 (pt0) REVERT: G 181 MET cc_start: 0.4903 (ttm) cc_final: 0.4447 (ttp) REVERT: G 196 LEU cc_start: 0.8395 (mp) cc_final: 0.8048 (mt) REVERT: G 282 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7076 (mp0) REVERT: G 284 ASP cc_start: 0.5657 (m-30) cc_final: 0.5348 (t0) REVERT: G 329 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.4921 (tmm) REVERT: G 353 ARG cc_start: 0.6053 (mtm180) cc_final: 0.5686 (ttm110) REVERT: G 397 MET cc_start: 0.6086 (mmm) cc_final: 0.5872 (mmm) REVERT: G 401 LYS cc_start: 0.7064 (mptt) cc_final: 0.6653 (mmmt) REVERT: G 403 ASN cc_start: 0.5790 (p0) cc_final: 0.5488 (t0) REVERT: G 417 MET cc_start: 0.5867 (mmt) cc_final: 0.5565 (tpp) REVERT: G 419 MET cc_start: 0.4014 (mmm) cc_final: 0.3736 (tpt) REVERT: G 420 HIS cc_start: 0.7548 (p90) cc_final: 0.7014 (p-80) REVERT: G 431 TYR cc_start: 0.6114 (m-80) cc_final: 0.5193 (m-10) REVERT: G 436 LYS cc_start: 0.6534 (mttt) cc_final: 0.6332 (mttp) REVERT: K 7 LYS cc_start: 0.7032 (mtpt) cc_final: 0.6373 (mmmt) REVERT: K 54 MET cc_start: 0.5092 (mtm) cc_final: 0.4441 (mtm) outliers start: 130 outliers final: 32 residues processed: 1036 average time/residue: 0.2349 time to fit residues: 376.3237 Evaluate side-chains 611 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 571 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 950 THR Chi-restraints excluded: chain A residue 1827 GLN Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 498 GLN Chi-restraints excluded: chain J residue 657 ASN Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 782 LYS Chi-restraints excluded: chain J residue 809 LEU Chi-restraints excluded: chain J residue 874 TRP Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain F residue 398 GLN Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain B residue 390 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1030 GLN A1086 ASN A1087 ASN A1190 ASN A1368 GLN A1635 HIS A1677 GLN ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 GLN A1856 ASN A1869 ASN A2054 GLN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 GLN H 316 GLN ** H 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS J 184 ASN ** J 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 GLN J 507 GLN J 578 GLN J 676 GLN J 733 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN F 201 ASN F 270 HIS F 292 GLN F 320 GLN F 419 GLN F 451 GLN K 38 ASN K 45 ASN K 75 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127097 restraints weight = 49654.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127596 restraints weight = 48508.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129413 restraints weight = 38004.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129400 restraints weight = 28990.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129687 restraints weight = 26180.545| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32504 Z= 0.201 Angle : 0.928 17.348 44659 Z= 0.437 Chirality : 0.071 1.401 5136 Planarity : 0.005 0.083 5181 Dihedral : 14.452 178.961 5657 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.84 % Favored : 93.90 % Rotamer: Outliers : 3.91 % Allowed : 14.23 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.09 % Twisted Proline : 1.46 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3475 helix: 2.77 (0.12), residues: 1821 sheet: -2.23 (0.24), residues: 363 loop : -2.14 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1595 TYR 0.039 0.002 TYR J 838 PHE 0.033 0.002 PHE J 616 TRP 0.018 0.002 TRP A 823 HIS 0.019 0.001 HIS J 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (32504) covalent geometry : angle 0.92754 / 0.44 (44659) hydrogen bonds : bond 0.05087 / 2.65 ( 1667) hydrogen bonds : angle 4.60115 / 1.83 ( 4772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 650 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 769 MET cc_start: 0.7728 (mmp) cc_final: 0.7312 (mmt) REVERT: A 778 LYS cc_start: 0.7327 (mmmt) cc_final: 0.4806 (mtmt) REVERT: A 926 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7162 (mtmm) REVERT: A 996 ASP cc_start: 0.8183 (t0) cc_final: 0.7913 (t70) REVERT: A 1017 ASP cc_start: 0.6268 (p0) cc_final: 0.6009 (p0) REVERT: A 1186 TYR cc_start: 0.7768 (t80) cc_final: 0.7556 (t80) REVERT: A 1214 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6120 (mmt180) REVERT: A 1253 LYS cc_start: 0.7703 (pttt) cc_final: 0.7183 (tptt) REVERT: A 1309 ILE cc_start: 0.8937 (mt) cc_final: 0.8735 (tt) REVERT: A 1347 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8242 (mtt180) REVERT: A 1404 HIS cc_start: 0.7336 (t70) cc_final: 0.7034 (t-90) REVERT: A 1413 SER cc_start: 0.8696 (m) cc_final: 0.8487 (p) REVERT: A 1417 GLN cc_start: 0.8301 (tp40) cc_final: 0.8077 (tp40) REVERT: A 1498 ASP cc_start: 0.7318 (p0) cc_final: 0.7053 (p0) REVERT: A 1615 ASN cc_start: 0.7873 (t0) cc_final: 0.7111 (p0) REVERT: A 1637 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7509 (pptt) REVERT: A 1689 ARG cc_start: 0.7357 (mtt90) cc_final: 0.7075 (mmt90) REVERT: A 1802 MET cc_start: 0.8217 (mmm) cc_final: 0.7823 (mmm) REVERT: A 1885 LYS cc_start: 0.8457 (tptt) cc_final: 0.8069 (mmtp) REVERT: A 1926 LYS cc_start: 0.7703 (mmmt) cc_final: 0.7420 (mmtt) REVERT: A 2055 MET cc_start: 0.7984 (mmt) cc_final: 0.7559 (mmt) REVERT: A 2078 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7745 (tm-30) REVERT: H 199 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8368 (pp) REVERT: H 225 ASP cc_start: 0.7228 (m-30) cc_final: 0.6879 (m-30) REVERT: H 234 MET cc_start: 0.8175 (ptm) cc_final: 0.7767 (ptm) REVERT: H 444 ASP cc_start: 0.7323 (t70) cc_final: 0.6843 (t0) REVERT: J 163 THR cc_start: 0.7944 (p) cc_final: 0.7680 (t) REVERT: J 221 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7639 (mt-10) REVERT: J 288 ASP cc_start: 0.4763 (OUTLIER) cc_final: 0.4273 (m-30) REVERT: J 340 LEU cc_start: 0.8404 (mt) cc_final: 0.8186 (mt) REVERT: J 347 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.5655 (m-10) REVERT: J 513 THR cc_start: 0.7670 (p) cc_final: 0.7380 (t) REVERT: J 553 MET cc_start: 0.7434 (tmm) cc_final: 0.7165 (tpp) REVERT: J 565 VAL cc_start: 0.7853 (t) cc_final: 0.7289 (m) REVERT: J 602 LYS cc_start: 0.6299 (mttt) cc_final: 0.5485 (tptm) REVERT: J 809 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8953 (tm) REVERT: J 810 GLU cc_start: 0.8194 (tp30) cc_final: 0.7564 (tp30) REVERT: D 71 ASP cc_start: 0.6690 (m-30) cc_final: 0.6149 (m-30) REVERT: F 120 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.6493 (t80) REVERT: F 155 ASP cc_start: 0.6145 (m-30) cc_final: 0.5839 (p0) REVERT: F 159 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7106 (m-10) REVERT: F 299 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.8496 (m170) REVERT: F 302 MET cc_start: 0.8257 (tpp) cc_final: 0.8045 (mmm) REVERT: G 393 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: G 431 TYR cc_start: 0.8270 (m-80) cc_final: 0.7073 (m-10) REVERT: K 32 GLN cc_start: 0.8288 (tp40) cc_final: 0.7648 (tt0) REVERT: K 106 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6142 (p0) outliers start: 120 outliers final: 50 residues processed: 734 average time/residue: 0.2171 time to fit residues: 253.1539 Evaluate side-chains 546 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 486 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1979 MET Chi-restraints excluded: chain A residue 1987 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 498 GLN Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain J residue 624 LEU Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 809 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain B residue 396 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 323 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 322 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1190 ASN A1568 ASN A1856 ASN A1907 GLN H 232 ASN ** H 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 ASN H 388 GLN J 285 HIS J 537 GLN ** J 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 641 ASN J 785 ASN ** J 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 201 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN G 276 ASN G 283 ASN G 300 GLN G 343 GLN G 433 GLN K 75 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.125709 restraints weight = 50137.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125447 restraints weight = 44630.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126301 restraints weight = 44998.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126806 restraints weight = 33353.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126926 restraints weight = 29951.406| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32504 Z= 0.202 Angle : 0.860 15.046 44659 Z= 0.405 Chirality : 0.062 0.955 5136 Planarity : 0.005 0.094 5181 Dihedral : 13.809 175.366 5609 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.70 % Favored : 94.07 % Rotamer: Outliers : 4.50 % Allowed : 16.64 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.09 % Twisted Proline : 1.46 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3475 helix: 2.32 (0.12), residues: 1831 sheet: -1.99 (0.25), residues: 348 loop : -1.88 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 353 TYR 0.022 0.002 TYR G 392 PHE 0.022 0.002 PHE J 541 TRP 0.027 0.002 TRP H 226 HIS 0.013 0.001 HIS J 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (32504) covalent geometry : angle 0.86024 / 0.41 (44659) hydrogen bonds : bond 0.04538 / 2.35 ( 1667) hydrogen bonds : angle 4.51291 / 1.79 ( 4772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 579 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 769 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: A 778 LYS cc_start: 0.7527 (mmmt) cc_final: 0.4923 (mtmt) REVERT: A 1098 VAL cc_start: 0.8941 (t) cc_final: 0.8735 (m) REVERT: A 1186 TYR cc_start: 0.7798 (t80) cc_final: 0.7320 (t80) REVERT: A 1214 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6065 (mmt180) REVERT: A 1253 LYS cc_start: 0.7633 (pttt) cc_final: 0.7387 (tptt) REVERT: A 1347 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8264 (mtt180) REVERT: A 1404 HIS cc_start: 0.7318 (t70) cc_final: 0.7097 (t-90) REVERT: A 1417 GLN cc_start: 0.8396 (tp-100) cc_final: 0.8158 (tp40) REVERT: A 1533 ASP cc_start: 0.7716 (m-30) cc_final: 0.7371 (m-30) REVERT: A 1585 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5279 (mmm) REVERT: A 1615 ASN cc_start: 0.7962 (t0) cc_final: 0.7185 (p0) REVERT: A 1637 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7696 (ttpt) REVERT: A 1703 MET cc_start: 0.7186 (ttp) cc_final: 0.6833 (ttp) REVERT: A 1802 MET cc_start: 0.8051 (mmm) cc_final: 0.7841 (mmm) REVERT: A 1862 VAL cc_start: 0.7034 (t) cc_final: 0.6834 (p) REVERT: A 1885 LYS cc_start: 0.8471 (tptt) cc_final: 0.8159 (mmtp) REVERT: A 2078 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7777 (tm-30) REVERT: H 127 TYR cc_start: 0.8170 (t80) cc_final: 0.7538 (t80) REVERT: H 138 LYS cc_start: 0.8414 (mmtp) cc_final: 0.8116 (ttpp) REVERT: H 175 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7610 (m) REVERT: H 225 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: H 234 MET cc_start: 0.8471 (ptm) cc_final: 0.8076 (ptm) REVERT: H 273 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: H 378 ILE cc_start: 0.5437 (OUTLIER) cc_final: 0.5173 (mt) REVERT: J 221 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7632 (mt-10) REVERT: J 347 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.5728 (m-10) REVERT: J 570 LYS cc_start: 0.6822 (mmtp) cc_final: 0.6241 (mmtm) REVERT: J 582 LEU cc_start: 0.8391 (tp) cc_final: 0.8189 (tp) REVERT: J 602 LYS cc_start: 0.6413 (mttt) cc_final: 0.5633 (tptm) REVERT: J 810 GLU cc_start: 0.8175 (tp30) cc_final: 0.7601 (tp30) REVERT: D 25 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7459 (mtm-85) REVERT: D 40 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6964 (ttm) REVERT: D 54 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8347 (ptp-170) REVERT: D 71 ASP cc_start: 0.6615 (m-30) cc_final: 0.6080 (m-30) REVERT: D 127 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7805 (p0) REVERT: F 70 THR cc_start: 0.7932 (m) cc_final: 0.7445 (m) REVERT: F 120 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.6332 (t80) REVERT: F 155 ASP cc_start: 0.6402 (m-30) cc_final: 0.6196 (p0) REVERT: F 159 PHE cc_start: 0.7672 (m-10) cc_final: 0.7196 (m-10) REVERT: F 199 GLU cc_start: 0.5396 (tt0) cc_final: 0.5183 (pt0) REVERT: F 201 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8161 (t0) REVERT: F 261 SER cc_start: 0.8770 (p) cc_final: 0.8428 (t) REVERT: G 194 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: G 329 MET cc_start: 0.7861 (tmm) cc_final: 0.6315 (mtt) REVERT: G 393 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: G 397 MET cc_start: 0.8090 (mmm) cc_final: 0.7528 (mmt) REVERT: K 87 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9054 (tp) outliers start: 138 outliers final: 59 residues processed: 672 average time/residue: 0.2146 time to fit residues: 230.7211 Evaluate side-chains 550 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 475 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1979 MET Chi-restraints excluded: chain A residue 1987 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 14 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 306 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 848 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 641 ASN J 668 HIS J 805 HIS ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 GLN G 343 GLN G 433 GLN K 75 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121481 restraints weight = 50253.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122183 restraints weight = 48449.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123151 restraints weight = 40895.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123222 restraints weight = 30584.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123335 restraints weight = 29520.113| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 32504 Z= 0.262 Angle : 0.881 15.433 44659 Z= 0.412 Chirality : 0.061 0.847 5136 Planarity : 0.005 0.097 5181 Dihedral : 13.668 174.756 5600 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.61 % Favored : 94.16 % Rotamer: Outliers : 5.24 % Allowed : 17.59 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.09 % Twisted Proline : 1.46 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3475 helix: 1.78 (0.12), residues: 1829 sheet: -1.90 (0.26), residues: 320 loop : -1.81 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1272 TYR 0.024 0.002 TYR G 392 PHE 0.042 0.002 PHE J 616 TRP 0.040 0.002 TRP J 471 HIS 0.009 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.26 (32504) covalent geometry : angle 0.88082 / 0.41 (44659) hydrogen bonds : bond 0.04756 / 2.45 ( 1667) hydrogen bonds : angle 4.62539 / 1.83 ( 4772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 509 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8834 (tt) REVERT: A 1049 LEU cc_start: 0.8439 (tp) cc_final: 0.7956 (tp) REVERT: A 1186 TYR cc_start: 0.7900 (t80) cc_final: 0.7440 (t80) REVERT: A 1214 ARG cc_start: 0.7595 (mtt180) cc_final: 0.6266 (mmt180) REVERT: A 1253 LYS cc_start: 0.8157 (pttt) cc_final: 0.7739 (tptt) REVERT: A 1404 HIS cc_start: 0.7300 (t70) cc_final: 0.7060 (t-90) REVERT: A 1533 ASP cc_start: 0.7608 (m-30) cc_final: 0.7265 (m-30) REVERT: A 1637 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7966 (ttpt) REVERT: A 1666 CYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7055 (t) REVERT: A 1885 LYS cc_start: 0.8524 (tptt) cc_final: 0.8220 (mmtp) REVERT: A 1905 LEU cc_start: 0.7795 (mt) cc_final: 0.7473 (mt) REVERT: A 2056 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7426 (ttp-110) REVERT: A 2078 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7769 (tm-30) REVERT: H 127 TYR cc_start: 0.8287 (t80) cc_final: 0.8022 (t80) REVERT: H 130 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6982 (pt0) REVERT: H 138 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8142 (ttpp) REVERT: H 175 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7509 (m) REVERT: H 225 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6920 (m-30) REVERT: H 234 MET cc_start: 0.8471 (ptm) cc_final: 0.8097 (ptm) REVERT: H 273 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: H 378 ILE cc_start: 0.5214 (OUTLIER) cc_final: 0.4980 (mt) REVERT: H 444 ASP cc_start: 0.7568 (t0) cc_final: 0.7313 (t0) REVERT: J 347 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5790 (m-80) REVERT: J 602 LYS cc_start: 0.6160 (mttt) cc_final: 0.5446 (tptp) REVERT: J 810 GLU cc_start: 0.8196 (tp30) cc_final: 0.7694 (tp30) REVERT: D 36 ASP cc_start: 0.7346 (t70) cc_final: 0.7028 (t0) REVERT: D 40 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6894 (ttm) REVERT: D 42 MET cc_start: 0.8207 (tpp) cc_final: 0.7927 (tpp) REVERT: D 54 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8434 (ptp-170) REVERT: D 80 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6424 (mmt) REVERT: D 127 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7889 (p0) REVERT: F 261 SER cc_start: 0.8755 (p) cc_final: 0.8402 (t) REVERT: G 251 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6336 (mmt) REVERT: G 386 GLU cc_start: 0.6842 (mp0) cc_final: 0.6512 (mt-10) REVERT: G 393 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: G 397 MET cc_start: 0.8115 (mmm) cc_final: 0.7674 (mmt) REVERT: G 431 TYR cc_start: 0.8097 (m-80) cc_final: 0.7814 (m-10) REVERT: K 17 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8254 (t) REVERT: K 21 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7800 (mp) REVERT: K 108 SER cc_start: 0.8950 (t) cc_final: 0.8160 (m) REVERT: B 423 ILE cc_start: 0.6108 (OUTLIER) cc_final: 0.5183 (pt) outliers start: 161 outliers final: 87 residues processed: 620 average time/residue: 0.2032 time to fit residues: 205.1602 Evaluate side-chains 555 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 450 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1666 CYS Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1972 ASP Chi-restraints excluded: chain A residue 1979 MET Chi-restraints excluded: chain A residue 1987 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 636 TYR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 783 HIS Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain J residue 891 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 380 ARG Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 432 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 267 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 346 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1618 ASN ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS J 820 GLN J 861 ASN J 897 ASN D 90 HIS D 138 ASN F 201 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 ASN G 300 GLN G 343 GLN G 448 GLN ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 GLN K 75 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123615 restraints weight = 50245.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124801 restraints weight = 44350.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126497 restraints weight = 34364.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126299 restraints weight = 26118.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126589 restraints weight = 24671.522| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32504 Z= 0.178 Angle : 0.803 16.544 44659 Z= 0.375 Chirality : 0.058 0.820 5136 Planarity : 0.005 0.097 5181 Dihedral : 13.632 177.962 5596 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.53 % Favored : 94.27 % Rotamer: Outliers : 4.69 % Allowed : 18.99 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3475 helix: 1.76 (0.12), residues: 1835 sheet: -1.71 (0.26), residues: 327 loop : -1.67 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 518 TYR 0.024 0.002 TYR G 392 PHE 0.023 0.002 PHE J 541 TRP 0.034 0.002 TRP H 226 HIS 0.007 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (32504) covalent geometry : angle 0.80309 / 0.38 (44659) hydrogen bonds : bond 0.04334 / 2.23 ( 1667) hydrogen bonds : angle 4.50459 / 1.78 ( 4772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 527 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9070 (tt) REVERT: A 1049 LEU cc_start: 0.8471 (tp) cc_final: 0.7981 (tp) REVERT: A 1186 TYR cc_start: 0.7823 (t80) cc_final: 0.7519 (t80) REVERT: A 1214 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6199 (mmt180) REVERT: A 1253 LYS cc_start: 0.8097 (pttt) cc_final: 0.7671 (tptt) REVERT: A 1347 ARG cc_start: 0.8530 (mtt180) cc_final: 0.8301 (mtt180) REVERT: A 1387 VAL cc_start: 0.9174 (m) cc_final: 0.8902 (t) REVERT: A 1390 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8804 (m) REVERT: A 1404 HIS cc_start: 0.7350 (t70) cc_final: 0.7005 (t-90) REVERT: A 1533 ASP cc_start: 0.7835 (m-30) cc_final: 0.7493 (m-30) REVERT: A 1585 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5302 (mmm) REVERT: A 1615 ASN cc_start: 0.7739 (t0) cc_final: 0.7009 (p0) REVERT: A 1885 LYS cc_start: 0.8551 (tptt) cc_final: 0.8170 (mmtp) REVERT: A 2078 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7659 (tm-30) REVERT: H 127 TYR cc_start: 0.8355 (t80) cc_final: 0.8053 (t80) REVERT: H 138 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8057 (ttpp) REVERT: H 175 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7537 (m) REVERT: H 225 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7056 (m-30) REVERT: H 273 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: H 292 TRP cc_start: 0.8758 (m100) cc_final: 0.8134 (m100) REVERT: H 378 ILE cc_start: 0.5224 (OUTLIER) cc_final: 0.4989 (mt) REVERT: H 444 ASP cc_start: 0.7525 (t0) cc_final: 0.7310 (t0) REVERT: J 347 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5853 (m-80) REVERT: J 372 LEU cc_start: 0.6676 (tp) cc_final: 0.6458 (tp) REVERT: J 602 LYS cc_start: 0.6644 (mttt) cc_final: 0.5782 (tptm) REVERT: J 810 GLU cc_start: 0.8149 (tp30) cc_final: 0.7622 (tp30) REVERT: D 54 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8559 (ptp-170) REVERT: D 127 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7874 (p0) REVERT: F 155 ASP cc_start: 0.6094 (OUTLIER) cc_final: 0.4714 (p0) REVERT: F 159 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.5556 (m-80) REVERT: F 261 SER cc_start: 0.8735 (p) cc_final: 0.8410 (t) REVERT: F 380 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6695 (ttp-170) REVERT: G 242 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8682 (tttp) REVERT: G 393 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: G 397 MET cc_start: 0.8173 (mmm) cc_final: 0.7734 (mmt) REVERT: K 62 GLU cc_start: 0.7740 (mp0) cc_final: 0.7149 (mt-10) REVERT: K 108 SER cc_start: 0.8899 (t) cc_final: 0.8114 (m) REVERT: B 387 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6342 (tm-30) REVERT: B 423 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5541 (pt) outliers start: 144 outliers final: 81 residues processed: 631 average time/residue: 0.2004 time to fit residues: 204.4511 Evaluate side-chains 556 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 459 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1972 ASP Chi-restraints excluded: chain A residue 1987 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 636 TYR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 380 ARG Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 242 LYS Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 423 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 164 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 168 optimal weight: 0.8980 chunk 300 optimal weight: 0.5980 chunk 296 optimal weight: 0.7980 chunk 311 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 861 GLN A1655 GLN A1856 ASN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS J 897 ASN F 201 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 GLN ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.151029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125841 restraints weight = 50059.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127755 restraints weight = 43184.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.128457 restraints weight = 33740.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128602 restraints weight = 25457.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128702 restraints weight = 24299.256| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32504 Z= 0.150 Angle : 0.774 17.189 44659 Z= 0.362 Chirality : 0.056 0.769 5136 Planarity : 0.005 0.106 5181 Dihedral : 13.545 175.744 5596 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 3.78 % Allowed : 20.39 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3475 helix: 1.72 (0.12), residues: 1840 sheet: -1.54 (0.26), residues: 326 loop : -1.60 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 518 TYR 0.028 0.002 TYR J 381 PHE 0.027 0.002 PHE F 158 TRP 0.040 0.002 TRP A1028 HIS 0.006 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (32504) covalent geometry : angle 0.77355 / 0.36 (44659) hydrogen bonds : bond 0.04173 / 2.16 ( 1667) hydrogen bonds : angle 4.44169 / 1.75 ( 4772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 526 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1049 LEU cc_start: 0.8353 (tp) cc_final: 0.7891 (tp) REVERT: A 1166 ASP cc_start: 0.7847 (m-30) cc_final: 0.7599 (t0) REVERT: A 1214 ARG cc_start: 0.7243 (mtt180) cc_final: 0.5889 (mmt180) REVERT: A 1253 LYS cc_start: 0.8073 (pttt) cc_final: 0.7671 (tptt) REVERT: A 1347 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8254 (mtt180) REVERT: A 1387 VAL cc_start: 0.9164 (m) cc_final: 0.8887 (t) REVERT: A 1390 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8799 (m) REVERT: A 1404 HIS cc_start: 0.7328 (t70) cc_final: 0.6960 (t-90) REVERT: A 1585 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5296 (mmm) REVERT: A 1615 ASN cc_start: 0.7745 (t0) cc_final: 0.7260 (p0) REVERT: A 1743 TYR cc_start: 0.8210 (t80) cc_final: 0.7982 (t80) REVERT: A 1785 ASP cc_start: 0.7577 (t0) cc_final: 0.7255 (t0) REVERT: A 1885 LYS cc_start: 0.8519 (tptt) cc_final: 0.8153 (mmtp) REVERT: A 2078 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7613 (tm-30) REVERT: H 138 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8146 (ttpp) REVERT: H 175 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7389 (t) REVERT: H 198 ASP cc_start: 0.7632 (p0) cc_final: 0.7084 (p0) REVERT: H 225 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6930 (m-30) REVERT: H 273 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: H 292 TRP cc_start: 0.8804 (m100) cc_final: 0.8174 (m100) REVERT: H 323 CYS cc_start: 0.8241 (t) cc_final: 0.8035 (t) REVERT: H 378 ILE cc_start: 0.5228 (OUTLIER) cc_final: 0.4994 (mt) REVERT: H 444 ASP cc_start: 0.7515 (t0) cc_final: 0.7192 (t0) REVERT: J 347 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: J 372 LEU cc_start: 0.6488 (tp) cc_final: 0.6149 (tp) REVERT: J 489 LEU cc_start: 0.1922 (OUTLIER) cc_final: 0.0936 (tt) REVERT: J 602 LYS cc_start: 0.6496 (mttt) cc_final: 0.5686 (tptt) REVERT: J 810 GLU cc_start: 0.8145 (tp30) cc_final: 0.7721 (tp30) REVERT: J 874 TRP cc_start: 0.8070 (t-100) cc_final: 0.7319 (t-100) REVERT: D 51 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6914 (mm-30) REVERT: D 54 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8426 (ptp-170) REVERT: F 155 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.4871 (p0) REVERT: F 159 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.5733 (m-80) REVERT: F 261 SER cc_start: 0.8678 (p) cc_final: 0.8406 (t) REVERT: F 380 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6503 (ttp-170) REVERT: G 242 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8693 (tttp) REVERT: G 306 ARG cc_start: 0.8369 (ttp80) cc_final: 0.7489 (mtm110) REVERT: G 353 ARG cc_start: 0.7367 (mtt90) cc_final: 0.7164 (mtt90) REVERT: G 393 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: G 397 MET cc_start: 0.8135 (mmm) cc_final: 0.7674 (mmt) REVERT: K 18 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7141 (tt0) REVERT: K 62 GLU cc_start: 0.7804 (mp0) cc_final: 0.7227 (mt-10) REVERT: K 108 SER cc_start: 0.8898 (t) cc_final: 0.8207 (m) REVERT: K 112 THR cc_start: 0.8428 (p) cc_final: 0.8170 (m) REVERT: K 120 LYS cc_start: 0.8604 (tppt) cc_final: 0.8344 (tppp) REVERT: B 387 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6391 (tm-30) REVERT: B 423 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.4881 (pt) outliers start: 116 outliers final: 71 residues processed: 610 average time/residue: 0.2027 time to fit residues: 199.4052 Evaluate side-chains 555 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 469 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1972 ASP Chi-restraints excluded: chain A residue 1987 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 636 TYR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 380 ARG Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 242 LYS Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 423 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 93 optimal weight: 4.9990 chunk 314 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 317 optimal weight: 0.1980 chunk 290 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 784 GLN ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS J 897 ASN G 276 ASN G 343 GLN ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN B 396 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127143 restraints weight = 50446.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128033 restraints weight = 46213.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129323 restraints weight = 36842.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129247 restraints weight = 28736.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129523 restraints weight = 27081.085| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32504 Z= 0.150 Angle : 0.765 16.928 44659 Z= 0.359 Chirality : 0.055 0.704 5136 Planarity : 0.005 0.108 5181 Dihedral : 13.435 175.723 5591 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 3.94 % Allowed : 21.47 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3475 helix: 1.75 (0.12), residues: 1828 sheet: -1.44 (0.26), residues: 326 loop : -1.46 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 428 TYR 0.025 0.002 TYR A1784 PHE 0.028 0.002 PHE F 158 TRP 0.049 0.002 TRP A1028 HIS 0.013 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (32504) covalent geometry : angle 0.76544 / 0.36 (44659) hydrogen bonds : bond 0.04085 / 2.12 ( 1667) hydrogen bonds : angle 4.44331 / 1.75 ( 4772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 498 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1049 LEU cc_start: 0.8208 (tp) cc_final: 0.7730 (tp) REVERT: A 1166 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7624 (t0) REVERT: A 1214 ARG cc_start: 0.7174 (mtt180) cc_final: 0.5843 (mmt180) REVERT: A 1253 LYS cc_start: 0.7964 (pttt) cc_final: 0.7643 (tptt) REVERT: A 1261 SER cc_start: 0.8722 (t) cc_final: 0.8452 (p) REVERT: A 1347 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8244 (mtt180) REVERT: A 1387 VAL cc_start: 0.9156 (m) cc_final: 0.8880 (t) REVERT: A 1390 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8815 (m) REVERT: A 1404 HIS cc_start: 0.7312 (t70) cc_final: 0.6928 (t-90) REVERT: A 1585 MET cc_start: 0.6125 (OUTLIER) cc_final: 0.5350 (mmm) REVERT: A 1615 ASN cc_start: 0.7706 (t0) cc_final: 0.7249 (p0) REVERT: A 1666 CYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6872 (t) REVERT: A 1743 TYR cc_start: 0.8252 (t80) cc_final: 0.7979 (t80) REVERT: A 1785 ASP cc_start: 0.7807 (t0) cc_final: 0.7456 (t0) REVERT: A 1885 LYS cc_start: 0.8578 (tptt) cc_final: 0.8119 (mmtp) REVERT: A 1992 TYR cc_start: 0.8344 (m-80) cc_final: 0.8048 (m-80) REVERT: A 2078 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7623 (tm-30) REVERT: H 127 TYR cc_start: 0.8207 (t80) cc_final: 0.7934 (t80) REVERT: H 138 LYS cc_start: 0.8565 (mmtp) cc_final: 0.8149 (ttpp) REVERT: H 162 MET cc_start: 0.8984 (mmm) cc_final: 0.8774 (mmt) REVERT: H 175 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7449 (t) REVERT: H 225 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: H 292 TRP cc_start: 0.8795 (m100) cc_final: 0.8265 (m100) REVERT: H 376 TRP cc_start: 0.5682 (p-90) cc_final: 0.4778 (p-90) REVERT: H 378 ILE cc_start: 0.5436 (OUTLIER) cc_final: 0.5221 (mt) REVERT: H 430 MET cc_start: 0.5963 (mmp) cc_final: 0.5716 (mmp) REVERT: H 444 ASP cc_start: 0.7500 (t0) cc_final: 0.7195 (t0) REVERT: J 347 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.5876 (m-80) REVERT: J 372 LEU cc_start: 0.6413 (tp) cc_final: 0.6108 (tp) REVERT: J 459 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7034 (mt) REVERT: J 489 LEU cc_start: 0.1915 (OUTLIER) cc_final: 0.0879 (tt) REVERT: J 518 ARG cc_start: 0.6222 (mmp80) cc_final: 0.5738 (mmm160) REVERT: J 602 LYS cc_start: 0.6225 (mttt) cc_final: 0.5645 (tptm) REVERT: J 810 GLU cc_start: 0.8139 (tp30) cc_final: 0.7759 (tp30) REVERT: J 874 TRP cc_start: 0.7986 (t-100) cc_final: 0.7454 (t-100) REVERT: D 10 ARG cc_start: 0.6335 (mtm-85) cc_final: 0.5900 (ttm-80) REVERT: D 51 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6940 (mm-30) REVERT: D 54 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8461 (ptp-170) REVERT: D 100 ASN cc_start: 0.8446 (m-40) cc_final: 0.8098 (m110) REVERT: F 155 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5340 (p0) REVERT: F 159 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.5635 (m-10) REVERT: F 261 SER cc_start: 0.8612 (p) cc_final: 0.8377 (t) REVERT: F 331 HIS cc_start: 0.8464 (m170) cc_final: 0.7980 (m170) REVERT: F 380 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6548 (ttp-170) REVERT: G 242 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8636 (tttp) REVERT: G 276 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8261 (t0) REVERT: G 306 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7472 (mtm110) REVERT: G 329 MET cc_start: 0.7657 (tmm) cc_final: 0.7306 (tmm) REVERT: G 393 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: G 397 MET cc_start: 0.8125 (mmm) cc_final: 0.7688 (mmt) REVERT: K 18 GLN cc_start: 0.7431 (tm-30) cc_final: 0.7115 (tt0) REVERT: K 62 GLU cc_start: 0.7454 (mp0) cc_final: 0.7043 (mt-10) REVERT: K 105 ASN cc_start: 0.8286 (t0) cc_final: 0.7896 (t0) REVERT: K 108 SER cc_start: 0.8759 (t) cc_final: 0.8129 (m) REVERT: K 112 THR cc_start: 0.8286 (p) cc_final: 0.8048 (m) REVERT: B 387 GLU cc_start: 0.6797 (tm-30) cc_final: 0.6400 (tm-30) outliers start: 121 outliers final: 77 residues processed: 588 average time/residue: 0.2061 time to fit residues: 197.0033 Evaluate side-chains 551 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 457 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1383 PHE Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1666 CYS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1972 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 636 TYR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 380 ARG Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain G residue 242 LYS Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 423 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 340 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 316 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN J 805 HIS J 897 ASN F 201 ASN K 18 GLN K 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126896 restraints weight = 50322.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128187 restraints weight = 46475.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129682 restraints weight = 34396.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129208 restraints weight = 26831.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129449 restraints weight = 26854.674| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32504 Z= 0.161 Angle : 0.769 16.236 44659 Z= 0.361 Chirality : 0.054 0.620 5136 Planarity : 0.005 0.113 5181 Dihedral : 13.403 176.099 5591 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % Rotamer: Outliers : 3.88 % Allowed : 21.63 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3475 helix: 1.69 (0.12), residues: 1837 sheet: -1.41 (0.26), residues: 330 loop : -1.44 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 518 TYR 0.025 0.002 TYR H 353 PHE 0.028 0.002 PHE F 158 TRP 0.061 0.002 TRP A1028 HIS 0.011 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (32504) covalent geometry : angle 0.76868 / 0.36 (44659) hydrogen bonds : bond 0.04113 / 2.12 ( 1667) hydrogen bonds : angle 4.43325 / 1.74 ( 4772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 477 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 LYS cc_start: 0.7602 (mmmt) cc_final: 0.7394 (mmtm) REVERT: A 1049 LEU cc_start: 0.8192 (tp) cc_final: 0.7717 (tp) REVERT: A 1214 ARG cc_start: 0.7191 (mtt180) cc_final: 0.5844 (mmt180) REVERT: A 1253 LYS cc_start: 0.8096 (pttt) cc_final: 0.7688 (tptt) REVERT: A 1261 SER cc_start: 0.8664 (t) cc_final: 0.8163 (p) REVERT: A 1387 VAL cc_start: 0.9168 (m) cc_final: 0.8891 (t) REVERT: A 1390 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8825 (m) REVERT: A 1404 HIS cc_start: 0.7320 (t70) cc_final: 0.6935 (t-90) REVERT: A 1486 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7821 (mtm180) REVERT: A 1585 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5385 (mmm) REVERT: A 1615 ASN cc_start: 0.7722 (t0) cc_final: 0.7219 (p0) REVERT: A 1666 CYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6866 (t) REVERT: A 1743 TYR cc_start: 0.8288 (t80) cc_final: 0.8009 (t80) REVERT: A 1785 ASP cc_start: 0.7731 (t0) cc_final: 0.7353 (t0) REVERT: A 1885 LYS cc_start: 0.8616 (tptt) cc_final: 0.8129 (mmtp) REVERT: A 2078 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7620 (tm-30) REVERT: H 138 LYS cc_start: 0.8570 (mmtp) cc_final: 0.8149 (ttpp) REVERT: H 175 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7632 (t) REVERT: H 225 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: H 232 ASN cc_start: 0.7139 (OUTLIER) cc_final: 0.6110 (p0) REVERT: H 273 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: H 292 TRP cc_start: 0.8787 (m100) cc_final: 0.8278 (m100) REVERT: H 376 TRP cc_start: 0.5675 (p-90) cc_final: 0.4865 (p-90) REVERT: H 378 ILE cc_start: 0.5544 (OUTLIER) cc_final: 0.5289 (mt) REVERT: H 444 ASP cc_start: 0.7537 (t0) cc_final: 0.7229 (t0) REVERT: J 347 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5867 (m-80) REVERT: J 372 LEU cc_start: 0.6513 (tp) cc_final: 0.6190 (tp) REVERT: J 459 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7078 (mt) REVERT: J 489 LEU cc_start: 0.1595 (OUTLIER) cc_final: 0.0803 (tt) REVERT: J 602 LYS cc_start: 0.6368 (mttt) cc_final: 0.5689 (tptt) REVERT: J 810 GLU cc_start: 0.8143 (tp30) cc_final: 0.7789 (tp30) REVERT: D 10 ARG cc_start: 0.6249 (mtm-85) cc_final: 0.5852 (ttm-80) REVERT: D 22 GLU cc_start: 0.7136 (tp30) cc_final: 0.6848 (tp30) REVERT: D 51 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6989 (mm-30) REVERT: D 54 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8494 (ptp-170) REVERT: D 100 ASN cc_start: 0.8415 (m-40) cc_final: 0.8084 (m110) REVERT: F 159 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6620 (m-10) REVERT: F 261 SER cc_start: 0.8629 (p) cc_final: 0.8391 (t) REVERT: F 331 HIS cc_start: 0.8470 (m170) cc_final: 0.7980 (m170) REVERT: G 242 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8666 (tttp) REVERT: G 306 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7487 (mtm110) REVERT: G 329 MET cc_start: 0.7755 (tmm) cc_final: 0.7386 (tmm) REVERT: G 353 ARG cc_start: 0.7492 (mtt90) cc_final: 0.6887 (mtt90) REVERT: G 393 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: G 397 MET cc_start: 0.8202 (mmm) cc_final: 0.7722 (mmt) REVERT: K 18 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: K 62 GLU cc_start: 0.7468 (mp0) cc_final: 0.7080 (mt-10) REVERT: K 105 ASN cc_start: 0.8336 (t0) cc_final: 0.8092 (t0) REVERT: K 108 SER cc_start: 0.8774 (t) cc_final: 0.8084 (m) REVERT: B 387 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6405 (tm-30) REVERT: B 423 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.5441 (pt) outliers start: 119 outliers final: 78 residues processed: 563 average time/residue: 0.2034 time to fit residues: 186.2783 Evaluate side-chains 541 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 446 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1383 PHE Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1666 CYS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1703 MET Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1972 ASP Chi-restraints excluded: chain A residue 1988 LEU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 637 TYR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 783 HIS Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 242 LYS Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 GLN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 423 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 200 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 366 optimal weight: 4.9990 chunk 314 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 274 HIS ** H 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS J 897 ASN D 99 ASN F 113 HIS ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126329 restraints weight = 50182.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128080 restraints weight = 44011.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129280 restraints weight = 32053.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128877 restraints weight = 25871.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129146 restraints weight = 25225.218| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32504 Z= 0.169 Angle : 0.774 15.331 44659 Z= 0.364 Chirality : 0.053 0.538 5136 Planarity : 0.005 0.123 5181 Dihedral : 13.351 176.287 5590 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.18 % Favored : 94.68 % Rotamer: Outliers : 3.71 % Allowed : 22.25 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3475 helix: 1.66 (0.12), residues: 1829 sheet: -1.40 (0.26), residues: 332 loop : -1.39 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 428 TYR 0.026 0.002 TYR H 353 PHE 0.030 0.002 PHE F 158 TRP 0.051 0.002 TRP A1028 HIS 0.010 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (32504) covalent geometry : angle 0.77440 / 0.36 (44659) hydrogen bonds : bond 0.04179 / 2.15 ( 1667) hydrogen bonds : angle 4.44812 / 1.75 ( 4772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 461 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 MET cc_start: 0.8026 (tpt) cc_final: 0.7505 (tpt) REVERT: A 1049 LEU cc_start: 0.8222 (tp) cc_final: 0.7730 (tp) REVERT: A 1214 ARG cc_start: 0.7214 (mtt180) cc_final: 0.5856 (mmt180) REVERT: A 1253 LYS cc_start: 0.8089 (pttt) cc_final: 0.7706 (tptt) REVERT: A 1261 SER cc_start: 0.8764 (t) cc_final: 0.8437 (p) REVERT: A 1387 VAL cc_start: 0.9163 (m) cc_final: 0.8894 (t) REVERT: A 1390 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8837 (m) REVERT: A 1404 HIS cc_start: 0.7334 (t70) cc_final: 0.6943 (t-90) REVERT: A 1486 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7745 (mtm180) REVERT: A 1585 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5433 (mmm) REVERT: A 1615 ASN cc_start: 0.7761 (t0) cc_final: 0.7219 (p0) REVERT: A 1666 CYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6802 (t) REVERT: A 1743 TYR cc_start: 0.8302 (t80) cc_final: 0.8069 (t80) REVERT: A 1785 ASP cc_start: 0.7968 (t0) cc_final: 0.7697 (t0) REVERT: A 1885 LYS cc_start: 0.8616 (tptt) cc_final: 0.8129 (mmtp) REVERT: A 2078 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7634 (tm-30) REVERT: H 138 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8114 (ttpp) REVERT: H 175 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7839 (t) REVERT: H 199 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8563 (pp) REVERT: H 225 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6913 (m-30) REVERT: H 232 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6230 (p0) REVERT: H 273 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: H 292 TRP cc_start: 0.8788 (m100) cc_final: 0.8287 (m100) REVERT: H 376 TRP cc_start: 0.5728 (p-90) cc_final: 0.4946 (p-90) REVERT: H 378 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.5378 (mt) REVERT: H 444 ASP cc_start: 0.7540 (t0) cc_final: 0.7244 (t0) REVERT: J 347 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.5882 (m-80) REVERT: J 372 LEU cc_start: 0.6552 (tp) cc_final: 0.6231 (tp) REVERT: J 459 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7202 (mt) REVERT: J 489 LEU cc_start: 0.1150 (OUTLIER) cc_final: 0.0417 (tt) REVERT: J 602 LYS cc_start: 0.6473 (mttt) cc_final: 0.5847 (tptt) REVERT: J 810 GLU cc_start: 0.8161 (tp30) cc_final: 0.7804 (tp30) REVERT: J 874 TRP cc_start: 0.8157 (t-100) cc_final: 0.7615 (t-100) REVERT: J 896 MET cc_start: 0.7140 (mmt) cc_final: 0.6929 (mmt) REVERT: D 10 ARG cc_start: 0.6320 (mtm-85) cc_final: 0.5861 (ttm-80) REVERT: D 22 GLU cc_start: 0.6899 (tp30) cc_final: 0.6695 (tp30) REVERT: D 51 GLU cc_start: 0.7245 (mm-30) cc_final: 0.7029 (mm-30) REVERT: D 54 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8500 (ptp-170) REVERT: D 100 ASN cc_start: 0.8421 (m-40) cc_final: 0.8120 (m-40) REVERT: F 159 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6690 (m-10) REVERT: F 261 SER cc_start: 0.8653 (p) cc_final: 0.8416 (t) REVERT: F 331 HIS cc_start: 0.8478 (m170) cc_final: 0.7986 (m170) REVERT: G 242 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8716 (tttp) REVERT: G 306 ARG cc_start: 0.8376 (ttp80) cc_final: 0.7491 (mtm110) REVERT: G 329 MET cc_start: 0.7750 (tmm) cc_final: 0.7392 (tmm) REVERT: G 353 ARG cc_start: 0.7569 (mtt90) cc_final: 0.7112 (mtt90) REVERT: G 393 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: G 397 MET cc_start: 0.8217 (mmm) cc_final: 0.7757 (mmt) REVERT: K 62 GLU cc_start: 0.7450 (mp0) cc_final: 0.7054 (mt-10) REVERT: K 104 THR cc_start: 0.8557 (m) cc_final: 0.8350 (p) REVERT: K 105 ASN cc_start: 0.8359 (t0) cc_final: 0.8141 (t0) REVERT: K 108 SER cc_start: 0.8808 (t) cc_final: 0.8098 (m) REVERT: B 387 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6404 (tm-30) REVERT: B 423 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5790 (pt) outliers start: 114 outliers final: 82 residues processed: 545 average time/residue: 0.2088 time to fit residues: 185.3444 Evaluate side-chains 541 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 442 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1383 PHE Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1666 CYS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1972 ASP Chi-restraints excluded: chain A residue 1988 LEU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain J residue 636 TYR Chi-restraints excluded: chain J residue 637 TYR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 783 HIS Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 242 LYS Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 423 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 100 optimal weight: 2.9990 chunk 245 optimal weight: 0.0000 chunk 232 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 323 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1737 GLN H 274 HIS ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS D 99 ASN F 201 ASN K 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126784 restraints weight = 50003.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127684 restraints weight = 44656.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128962 restraints weight = 34348.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128977 restraints weight = 27924.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130007 restraints weight = 25863.213| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32504 Z= 0.164 Angle : 0.777 14.773 44659 Z= 0.366 Chirality : 0.053 0.515 5136 Planarity : 0.005 0.120 5181 Dihedral : 13.340 176.399 5590 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.18 % Favored : 94.68 % Rotamer: Outliers : 3.49 % Allowed : 22.57 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3475 helix: 1.63 (0.12), residues: 1827 sheet: -1.47 (0.26), residues: 338 loop : -1.35 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG F 428 TYR 0.030 0.002 TYR H 353 PHE 0.031 0.002 PHE F 158 TRP 0.046 0.002 TRP A1028 HIS 0.010 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (32504) covalent geometry : angle 0.77667 / 0.37 (44659) hydrogen bonds : bond 0.04144 / 2.14 ( 1667) hydrogen bonds : angle 4.45196 / 1.74 ( 4772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 466 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 MET cc_start: 0.8004 (tpt) cc_final: 0.7486 (tpt) REVERT: A 926 LYS cc_start: 0.8059 (ptpp) cc_final: 0.7831 (mtmm) REVERT: A 1049 LEU cc_start: 0.8200 (tp) cc_final: 0.7717 (tp) REVERT: A 1214 ARG cc_start: 0.7213 (mtt180) cc_final: 0.5847 (mmt180) REVERT: A 1253 LYS cc_start: 0.8089 (pttt) cc_final: 0.7722 (tptt) REVERT: A 1261 SER cc_start: 0.8752 (t) cc_final: 0.8385 (p) REVERT: A 1387 VAL cc_start: 0.9157 (m) cc_final: 0.8887 (t) REVERT: A 1390 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8842 (m) REVERT: A 1404 HIS cc_start: 0.7322 (t70) cc_final: 0.6929 (t-90) REVERT: A 1585 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5472 (mmm) REVERT: A 1615 ASN cc_start: 0.7757 (t0) cc_final: 0.7229 (p0) REVERT: A 1666 CYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6765 (t) REVERT: A 1743 TYR cc_start: 0.8332 (t80) cc_final: 0.8055 (t80) REVERT: A 1785 ASP cc_start: 0.7977 (t0) cc_final: 0.7604 (t0) REVERT: A 1843 LEU cc_start: 0.8465 (mt) cc_final: 0.8110 (tt) REVERT: A 1885 LYS cc_start: 0.8622 (tptt) cc_final: 0.8098 (mmtp) REVERT: A 2078 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7636 (tm-30) REVERT: H 138 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8105 (ttpp) REVERT: H 175 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7820 (t) REVERT: H 199 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8606 (pp) REVERT: H 225 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7034 (m-30) REVERT: H 232 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6255 (p0) REVERT: H 273 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: H 292 TRP cc_start: 0.8776 (m100) cc_final: 0.8271 (m100) REVERT: H 376 TRP cc_start: 0.5712 (p-90) cc_final: 0.4921 (p-90) REVERT: H 378 ILE cc_start: 0.5647 (OUTLIER) cc_final: 0.5421 (mt) REVERT: H 408 LYS cc_start: 0.4906 (mttt) cc_final: 0.4676 (mttp) REVERT: H 444 ASP cc_start: 0.7540 (t0) cc_final: 0.7267 (t0) REVERT: J 347 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.5857 (m-80) REVERT: J 372 LEU cc_start: 0.6518 (tp) cc_final: 0.6185 (tp) REVERT: J 459 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6934 (mt) REVERT: J 489 LEU cc_start: 0.1190 (OUTLIER) cc_final: 0.0411 (tt) REVERT: J 554 ARG cc_start: 0.7184 (mtp180) cc_final: 0.6679 (ttm170) REVERT: J 602 LYS cc_start: 0.6361 (mttt) cc_final: 0.5702 (tptt) REVERT: J 810 GLU cc_start: 0.8000 (tp30) cc_final: 0.7695 (tp30) REVERT: J 874 TRP cc_start: 0.8164 (t-100) cc_final: 0.7609 (t-100) REVERT: J 896 MET cc_start: 0.7179 (mmt) cc_final: 0.6962 (mmt) REVERT: D 10 ARG cc_start: 0.6484 (mtm-85) cc_final: 0.6034 (ttm-80) REVERT: D 51 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6967 (mm-30) REVERT: D 54 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8249 (ptp-170) REVERT: D 100 ASN cc_start: 0.8475 (m-40) cc_final: 0.8013 (m110) REVERT: F 97 PHE cc_start: 0.7430 (m-80) cc_final: 0.6885 (t80) REVERT: F 159 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.6736 (m-10) REVERT: F 261 SER cc_start: 0.8653 (p) cc_final: 0.8413 (t) REVERT: F 331 HIS cc_start: 0.8464 (m170) cc_final: 0.8086 (m170) REVERT: F 428 ARG cc_start: 0.7442 (ttp80) cc_final: 0.6992 (ttp80) REVERT: G 242 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8656 (tttp) REVERT: G 306 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7495 (mtm110) REVERT: G 329 MET cc_start: 0.7739 (tmm) cc_final: 0.7375 (tmm) REVERT: G 353 ARG cc_start: 0.7552 (mtt90) cc_final: 0.7077 (mtt90) REVERT: G 393 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: G 397 MET cc_start: 0.8220 (mmm) cc_final: 0.7806 (mmt) REVERT: K 62 GLU cc_start: 0.7552 (mp0) cc_final: 0.7158 (mt-10) REVERT: K 104 THR cc_start: 0.8558 (m) cc_final: 0.8319 (p) REVERT: K 105 ASN cc_start: 0.8357 (t0) cc_final: 0.8148 (t0) REVERT: K 108 SER cc_start: 0.8814 (t) cc_final: 0.8101 (m) REVERT: B 387 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6481 (tm-30) outliers start: 107 outliers final: 80 residues processed: 547 average time/residue: 0.2067 time to fit residues: 184.0943 Evaluate side-chains 537 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 441 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1637 LYS Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1666 CYS Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1972 ASP Chi-restraints excluded: chain A residue 1988 LEU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 378 ILE Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 347 PHE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 617 PHE Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 242 LYS Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 380 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 46 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 chunk 340 optimal weight: 0.9980 chunk 328 optimal weight: 0.0030 chunk 267 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 977 ASN H 274 HIS ** H 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS J 861 ASN D 99 ASN K 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128231 restraints weight = 50392.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127922 restraints weight = 42278.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128556 restraints weight = 41025.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129111 restraints weight = 32124.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129253 restraints weight = 28943.713| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32504 Z= 0.147 Angle : 0.765 14.155 44659 Z= 0.360 Chirality : 0.052 0.598 5136 Planarity : 0.005 0.129 5181 Dihedral : 13.275 176.516 5590 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.98 % Favored : 94.88 % Rotamer: Outliers : 3.68 % Allowed : 22.28 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3475 helix: 1.62 (0.12), residues: 1827 sheet: -1.40 (0.26), residues: 339 loop : -1.23 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 428 TYR 0.030 0.002 TYR H 353 PHE 0.032 0.002 PHE F 158 TRP 0.046 0.002 TRP A1028 HIS 0.009 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (32504) covalent geometry : angle 0.76460 / 0.36 (44659) hydrogen bonds : bond 0.04028 / 2.08 ( 1667) hydrogen bonds : angle 4.42359 / 1.73 ( 4772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5796.91 seconds wall clock time: 101 minutes 26.48 seconds (6086.48 seconds total)