Starting phenix.real_space_refine on Sun Sep 29 01:53:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tlj_10516/09_2024/6tlj_10516.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tlj_10516/09_2024/6tlj_10516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tlj_10516/09_2024/6tlj_10516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tlj_10516/09_2024/6tlj_10516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tlj_10516/09_2024/6tlj_10516.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tlj_10516/09_2024/6tlj_10516.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 50 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 418 5.16 5 C 46193 2.51 5 N 12436 2.21 5 O 13258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 333 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72305 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 10949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1441, 10949 Classifications: {'peptide': 1441} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 107} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 78, 'TRANS': 1358} Chain breaks: 20 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 224 Chain: "B" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 643 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain breaks: 1 Chain: "C" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4306 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 509} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 153 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 450 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3849 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 213 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3853 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5728 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 707} Chain breaks: 2 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "J" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4047 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "K" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3988 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1435 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 493 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain breaks: 1 Chain: "N" Number of atoms: 5403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5403 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'CIS': 16, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 654} Chain breaks: 9 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 196 Chain: "O" Number of atoms: 5402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5402 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4043 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 477} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2739 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 346} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "R" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2953 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 361} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2227 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 273} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "W" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 213 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3773 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3868 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Z" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1577 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Time building chain proxies: 30.72, per 1000 atoms: 0.42 Number of scatterers: 72305 At special positions: 0 Unit cell: (231.2, 199.92, 224.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 418 16.00 O 13258 8.00 N 12436 7.00 C 46193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 44 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 79 " - pdb=" SG CYS Z 106 " distance=2.04 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: 14.33 Conformation dependent library (CDL) restraints added in 7.1 seconds 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17558 Finding SS restraints... Secondary structure from input PDB file: 406 helices and 41 sheets defined 64.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.55 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 removed outlier: 4.017A pdb=" N ASP A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 360 removed outlier: 4.056A pdb=" N HIS A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 631 through 647 removed outlier: 3.767A pdb=" N VAL A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.895A pdb=" N ILE A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 798 removed outlier: 3.889A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 925 through 937 Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 948 through 964 Proline residue: A 954 - end of helix removed outlier: 3.594A pdb=" N ALA A 958 " --> pdb=" O PRO A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 978 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1032 through 1042 removed outlier: 3.709A pdb=" N ASP A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 3.813A pdb=" N GLU A1064 " --> pdb=" O HIS A1060 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1088 Processing helix chain 'A' and resid 1132 through 1146 Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 3.662A pdb=" N ILE A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1183 Processing helix chain 'A' and resid 1184 through 1188 Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.278A pdb=" N ASP A1195 " --> pdb=" O LEU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 removed outlier: 3.588A pdb=" N LYS A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1230 Processing helix chain 'A' and resid 1246 through 1261 removed outlier: 3.583A pdb=" N VAL A1251 " --> pdb=" O HIS A1247 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A1252 " --> pdb=" O ASN A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 4.155A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.782A pdb=" N TYR A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 Processing helix chain 'A' and resid 1359 through 1375 removed outlier: 3.828A pdb=" N THR A1363 " --> pdb=" O ASN A1359 " (cutoff:3.500A) Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1380 through 1386 Processing helix chain 'A' and resid 1394 through 1398 Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.746A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1428 removed outlier: 3.826A pdb=" N VAL A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1437 removed outlier: 4.597A pdb=" N ASN A1437 " --> pdb=" O ILE A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1477 Processing helix chain 'A' and resid 1481 through 1500 Processing helix chain 'A' and resid 1503 through 1508 Processing helix chain 'A' and resid 1508 through 1527 Processing helix chain 'A' and resid 1532 through 1545 removed outlier: 4.213A pdb=" N LEU A1538 " --> pdb=" O LYS A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1567 Processing helix chain 'A' and resid 1578 through 1589 Processing helix chain 'A' and resid 1603 through 1613 removed outlier: 3.861A pdb=" N HIS A1608 " --> pdb=" O ALA A1605 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A1610 " --> pdb=" O ARG A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1661 No H-bonds generated for 'chain 'A' and resid 1659 through 1661' Processing helix chain 'A' and resid 1685 through 1693 Processing helix chain 'A' and resid 1744 through 1755 Processing helix chain 'A' and resid 1764 through 1781 removed outlier: 3.888A pdb=" N LEU A1768 " --> pdb=" O LYS A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1803 Processing helix chain 'A' and resid 1808 through 1823 removed outlier: 3.720A pdb=" N GLN A1813 " --> pdb=" O SER A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1844 through 1863 Processing helix chain 'A' and resid 1864 through 1872 Processing helix chain 'A' and resid 1881 through 1893 removed outlier: 3.700A pdb=" N CYS A1887 " --> pdb=" O SER A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1922 Processing helix chain 'A' and resid 1927 through 1936 Proline residue: A1933 - end of helix Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'C' and resid 28 through 47 removed outlier: 4.544A pdb=" N LYS C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 62 removed outlier: 3.806A pdb=" N LEU C 58 " --> pdb=" O TRP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 83 through 97 removed outlier: 4.442A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.603A pdb=" N VAL C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 136 " --> pdb=" O ASP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 164 removed outlier: 4.059A pdb=" N VAL C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'C' and resid 184 through 199 removed outlier: 3.584A pdb=" N ASP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.780A pdb=" N TRP C 206 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.621A pdb=" N PHE C 232 " --> pdb=" O TRP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 262 through 276 Processing helix chain 'C' and resid 278 through 293 Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 312 through 327 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 346 through 361 Processing helix chain 'C' and resid 365 through 378 removed outlier: 3.770A pdb=" N THR C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 414 through 429 removed outlier: 4.241A pdb=" N TYR C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR C 421 " --> pdb=" O TYR C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.581A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 463 Processing helix chain 'C' and resid 468 through 480 Processing helix chain 'C' and resid 482 through 500 Processing helix chain 'C' and resid 510 through 523 Processing helix chain 'C' and resid 525 through 540 removed outlier: 3.625A pdb=" N CYS C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 557 removed outlier: 4.164A pdb=" N LYS C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 92 removed outlier: 4.175A pdb=" N GLU E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 20 through 36 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 53 through 64 Processing helix chain 'F' and resid 68 through 82 Processing helix chain 'F' and resid 84 through 94 removed outlier: 4.215A pdb=" N LEU F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 130 through 145 removed outlier: 3.721A pdb=" N ASN F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 452 through 478 removed outlier: 3.741A pdb=" N ALA F 458 " --> pdb=" O LEU F 454 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU F 462 " --> pdb=" O ALA F 458 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU F 465 " --> pdb=" O GLY F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 490 removed outlier: 3.529A pdb=" N HIS F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 513 Processing helix chain 'F' and resid 514 through 529 Processing helix chain 'F' and resid 535 through 547 Processing helix chain 'F' and resid 548 through 563 Processing helix chain 'F' and resid 566 through 580 removed outlier: 4.048A pdb=" N TRP F 570 " --> pdb=" O SER F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 597 Processing helix chain 'F' and resid 600 through 614 removed outlier: 4.316A pdb=" N TYR F 604 " --> pdb=" O TYR F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 631 removed outlier: 3.560A pdb=" N ALA F 622 " --> pdb=" O ASP F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 648 removed outlier: 3.906A pdb=" N TRP F 638 " --> pdb=" O HIS F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 665 removed outlier: 3.622A pdb=" N MET F 656 " --> pdb=" O SER F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 668 through 682 Processing helix chain 'F' and resid 684 through 699 Processing helix chain 'F' and resid 702 through 716 Processing helix chain 'F' and resid 718 through 733 removed outlier: 3.865A pdb=" N GLU F 728 " --> pdb=" O GLN F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 751 removed outlier: 3.745A pdb=" N TYR F 740 " --> pdb=" O GLU F 736 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS F 749 " --> pdb=" O LYS F 745 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 766 Processing helix chain 'G' and resid 12 through 24 removed outlier: 4.457A pdb=" N GLU G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 20 through 36 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 53 through 64 Processing helix chain 'H' and resid 68 through 82 Processing helix chain 'H' and resid 84 through 94 removed outlier: 3.521A pdb=" N LEU H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 113 through 128 Processing helix chain 'H' and resid 130 through 145 Processing helix chain 'H' and resid 148 through 158 removed outlier: 4.028A pdb=" N PHE H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 452 through 478 removed outlier: 3.709A pdb=" N ALA H 458 " --> pdb=" O LEU H 454 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU H 462 " --> pdb=" O ALA H 458 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU H 465 " --> pdb=" O GLY H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 490 removed outlier: 3.777A pdb=" N HIS H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 513 Processing helix chain 'H' and resid 514 through 529 Processing helix chain 'H' and resid 535 through 547 Processing helix chain 'H' and resid 548 through 563 Processing helix chain 'H' and resid 566 through 581 removed outlier: 3.765A pdb=" N TRP H 570 " --> pdb=" O SER H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 597 Processing helix chain 'H' and resid 600 through 615 removed outlier: 4.037A pdb=" N TYR H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 631 removed outlier: 4.253A pdb=" N ALA H 622 " --> pdb=" O ASP H 618 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS H 623 " --> pdb=" O LYS H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 648 removed outlier: 3.797A pdb=" N TRP H 638 " --> pdb=" O HIS H 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 665 removed outlier: 3.710A pdb=" N MET H 656 " --> pdb=" O SER H 652 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 682 Processing helix chain 'H' and resid 684 through 699 Processing helix chain 'H' and resid 702 through 716 removed outlier: 4.076A pdb=" N LYS H 706 " --> pdb=" O ASN H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 733 removed outlier: 3.830A pdb=" N GLU H 728 " --> pdb=" O GLN H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 736 through 751 removed outlier: 3.995A pdb=" N TYR H 740 " --> pdb=" O GLU H 736 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 767 Processing helix chain 'I' and resid 49 through 52 Processing helix chain 'I' and resid 119 through 124 Processing helix chain 'I' and resid 161 through 170 removed outlier: 3.712A pdb=" N ILE I 165 " --> pdb=" O SER I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 244 removed outlier: 3.762A pdb=" N TYR I 242 " --> pdb=" O THR I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 294 removed outlier: 3.561A pdb=" N ALA I 275 " --> pdb=" O CYS I 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU I 277 " --> pdb=" O CYS I 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU I 278 " --> pdb=" O GLU I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 310 removed outlier: 3.885A pdb=" N GLU I 303 " --> pdb=" O SER I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 325 Processing helix chain 'I' and resid 326 through 372 removed outlier: 4.212A pdb=" N GLN I 353 " --> pdb=" O ILE I 349 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER I 354 " --> pdb=" O SER I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'I' and resid 382 through 429 removed outlier: 4.057A pdb=" N ARG I 419 " --> pdb=" O LYS I 415 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP I 420 " --> pdb=" O ALA I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 456 Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.556A pdb=" N LEU I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 521 through 548 Proline residue: I 540 - end of helix Processing helix chain 'I' and resid 671 through 675 Processing helix chain 'I' and resid 679 through 683 Processing helix chain 'J' and resid 3 through 17 Processing helix chain 'J' and resid 18 through 33 Processing helix chain 'J' and resid 36 through 50 removed outlier: 4.043A pdb=" N TRP J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 62 Processing helix chain 'J' and resid 64 through 70 Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.904A pdb=" N LEU J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 94 Processing helix chain 'J' and resid 125 through 143 Processing helix chain 'J' and resid 145 through 160 removed outlier: 3.876A pdb=" N TYR J 151 " --> pdb=" O THR J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 173 Processing helix chain 'J' and resid 177 through 188 removed outlier: 3.536A pdb=" N GLU J 186 " --> pdb=" O LYS J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 209 Processing helix chain 'J' and resid 230 through 245 Processing helix chain 'J' and resid 246 through 261 removed outlier: 3.806A pdb=" N VAL J 256 " --> pdb=" O LYS J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 279 Processing helix chain 'J' and resid 280 through 295 Processing helix chain 'J' and resid 298 through 313 removed outlier: 4.320A pdb=" N TRP J 302 " --> pdb=" O ASN J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 330 Processing helix chain 'J' and resid 333 through 348 removed outlier: 3.788A pdb=" N TRP J 337 " --> pdb=" O TYR J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 364 Processing helix chain 'J' and resid 368 through 381 Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 401 through 416 Processing helix chain 'J' and resid 418 through 433 Processing helix chain 'J' and resid 444 through 459 Processing helix chain 'J' and resid 460 through 475 Processing helix chain 'J' and resid 478 through 493 Processing helix chain 'J' and resid 494 through 509 Processing helix chain 'J' and resid 512 through 529 Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 62 Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 128 through 143 removed outlier: 4.148A pdb=" N CYS K 133 " --> pdb=" O LYS K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 161 Processing helix chain 'K' and resid 164 through 172 Processing helix chain 'K' and resid 178 through 188 Processing helix chain 'K' and resid 194 through 211 removed outlier: 3.915A pdb=" N LYS K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS K 211 " --> pdb=" O ASN K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 225 removed outlier: 3.804A pdb=" N GLU K 222 " --> pdb=" O THR K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 229 removed outlier: 3.509A pdb=" N GLU K 229 " --> pdb=" O GLY K 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 226 through 229' Processing helix chain 'K' and resid 230 through 245 Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 267 through 279 Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 299 through 313 removed outlier: 3.798A pdb=" N GLY K 313 " --> pdb=" O TYR K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 Processing helix chain 'K' and resid 333 through 348 removed outlier: 4.110A pdb=" N TRP K 337 " --> pdb=" O TYR K 333 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE K 344 " --> pdb=" O TYR K 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 364 Processing helix chain 'K' and resid 368 through 381 Processing helix chain 'K' and resid 383 through 398 removed outlier: 3.535A pdb=" N ILE K 397 " --> pdb=" O GLN K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 416 Processing helix chain 'K' and resid 417 through 435 Processing helix chain 'K' and resid 440 through 459 removed outlier: 4.019A pdb=" N TRP K 444 " --> pdb=" O THR K 440 " (cutoff:3.500A) Proline residue: K 446 - end of helix Processing helix chain 'K' and resid 460 through 475 removed outlier: 3.520A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 493 Processing helix chain 'K' and resid 494 through 509 removed outlier: 3.570A pdb=" N ASP K 500 " --> pdb=" O GLU K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 527 Processing helix chain 'L' and resid 12 through 19 removed outlier: 3.894A pdb=" N LEU L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'M' and resid 8 through 16 removed outlier: 4.530A pdb=" N ASP M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'N' and resid 16 through 28 Processing helix chain 'N' and resid 54 through 63 Processing helix chain 'N' and resid 75 through 92 removed outlier: 4.943A pdb=" N ASN N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Proline residue: N 89 - end of helix Processing helix chain 'N' and resid 94 through 100 removed outlier: 3.789A pdb=" N ASN N 100 " --> pdb=" O SER N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 123 Processing helix chain 'N' and resid 126 through 139 Processing helix chain 'N' and resid 149 through 162 Processing helix chain 'N' and resid 166 through 191 Processing helix chain 'N' and resid 203 through 215 Processing helix chain 'N' and resid 234 through 250 removed outlier: 3.651A pdb=" N LEU N 250 " --> pdb=" O VAL N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 278 removed outlier: 4.591A pdb=" N GLU N 259 " --> pdb=" O ARG N 255 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA N 260 " --> pdb=" O VAL N 256 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG N 276 " --> pdb=" O ARG N 272 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 304 removed outlier: 5.490A pdb=" N ILE N 293 " --> pdb=" O PHE N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 343 Processing helix chain 'N' and resid 343 through 350 removed outlier: 3.543A pdb=" N ASP N 350 " --> pdb=" O SER N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 366 Processing helix chain 'N' and resid 370 through 386 Processing helix chain 'N' and resid 396 through 409 Processing helix chain 'N' and resid 410 through 413 Processing helix chain 'N' and resid 414 through 421 removed outlier: 3.541A pdb=" N GLU N 418 " --> pdb=" O MET N 414 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL N 419 " --> pdb=" O VAL N 415 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 431 Processing helix chain 'N' and resid 433 through 442 removed outlier: 3.734A pdb=" N GLN N 437 " --> pdb=" O ASP N 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 452 through 458 removed outlier: 3.888A pdb=" N ASP N 458 " --> pdb=" O GLU N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 509 Processing helix chain 'N' and resid 512 through 529 Processing helix chain 'N' and resid 535 through 549 Processing helix chain 'N' and resid 554 through 580 removed outlier: 4.172A pdb=" N MET N 560 " --> pdb=" O PHE N 556 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU N 561 " --> pdb=" O CYS N 557 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET N 564 " --> pdb=" O MET N 560 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA N 565 " --> pdb=" O LEU N 561 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP N 566 " --> pdb=" O LYS N 562 " (cutoff:3.500A) Processing helix chain 'N' and resid 612 through 630 removed outlier: 3.781A pdb=" N ALA N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS N 630 " --> pdb=" O TYR N 626 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 642 Processing helix chain 'N' and resid 660 through 672 Processing helix chain 'N' and resid 677 through 686 Processing helix chain 'N' and resid 688 through 703 Processing helix chain 'N' and resid 748 through 766 Processing helix chain 'N' and resid 769 through 781 Processing helix chain 'N' and resid 791 through 805 Processing helix chain 'O' and resid 31 through 45 Processing helix chain 'O' and resid 53 through 70 Proline residue: O 66 - end of helix Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'O' and resid 86 through 103 removed outlier: 3.666A pdb=" N ALA O 90 " --> pdb=" O CYS O 86 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN O 91 " --> pdb=" O PRO O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 121 removed outlier: 3.988A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER O 120 " --> pdb=" O SER O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 146 Processing helix chain 'O' and resid 147 through 169 removed outlier: 4.021A pdb=" N THR O 169 " --> pdb=" O GLY O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 225 removed outlier: 4.228A pdb=" N PHE O 214 " --> pdb=" O LYS O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 247 Processing helix chain 'O' and resid 251 through 265 removed outlier: 3.733A pdb=" N TYR O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 281 Processing helix chain 'O' and resid 299 through 314 Processing helix chain 'O' and resid 316 through 334 removed outlier: 3.563A pdb=" N LEU O 322 " --> pdb=" O GLN O 318 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 351 Processing helix chain 'O' and resid 358 through 370 removed outlier: 4.151A pdb=" N LYS O 366 " --> pdb=" O GLU O 362 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 392 Processing helix chain 'O' and resid 394 through 413 removed outlier: 3.815A pdb=" N LEU O 408 " --> pdb=" O ASP O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 432 Processing helix chain 'O' and resid 434 through 448 Processing helix chain 'O' and resid 464 through 480 Processing helix chain 'O' and resid 482 through 497 Processing helix chain 'O' and resid 503 through 523 removed outlier: 4.219A pdb=" N TRP O 507 " --> pdb=" O HIS O 503 " (cutoff:3.500A) Processing helix chain 'O' and resid 524 through 539 removed outlier: 3.863A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 554 Processing helix chain 'O' and resid 556 through 575 Processing helix chain 'O' and resid 576 through 594 Processing helix chain 'O' and resid 596 through 598 No H-bonds generated for 'chain 'O' and resid 596 through 598' Processing helix chain 'O' and resid 599 through 614 removed outlier: 4.620A pdb=" N MET O 603 " --> pdb=" O ILE O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 616 through 635 removed outlier: 3.894A pdb=" N GLU O 622 " --> pdb=" O TYR O 618 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 654 removed outlier: 3.962A pdb=" N MET O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA O 647 " --> pdb=" O LEU O 643 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU O 649 " --> pdb=" O HIS O 645 " (cutoff:3.500A) Proline residue: O 650 - end of helix Processing helix chain 'O' and resid 656 through 678 Processing helix chain 'O' and resid 682 through 705 removed outlier: 3.628A pdb=" N ALA O 689 " --> pdb=" O GLU O 685 " (cutoff:3.500A) Processing helix chain 'O' and resid 707 through 725 removed outlier: 4.007A pdb=" N ASP O 712 " --> pdb=" O GLU O 708 " (cutoff:3.500A) Processing helix chain 'O' and resid 726 through 741 Processing helix chain 'P' and resid 28 through 47 Processing helix chain 'P' and resid 48 through 62 Processing helix chain 'P' and resid 77 through 83 Processing helix chain 'P' and resid 83 through 97 removed outlier: 4.308A pdb=" N LYS P 97 " --> pdb=" O TYR P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 107 Processing helix chain 'P' and resid 111 through 134 Processing helix chain 'P' and resid 148 through 165 removed outlier: 3.950A pdb=" N ARG P 152 " --> pdb=" O ASN P 148 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU P 153 " --> pdb=" O GLU P 149 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 182 removed outlier: 3.697A pdb=" N TYR P 173 " --> pdb=" O GLY P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 199 removed outlier: 4.144A pdb=" N ASP P 190 " --> pdb=" O LYS P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 213 removed outlier: 3.819A pdb=" N TRP P 206 " --> pdb=" O HIS P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 222 Processing helix chain 'P' and resid 228 through 241 removed outlier: 3.926A pdb=" N PHE P 232 " --> pdb=" O TRP P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 257 Processing helix chain 'P' and resid 258 through 261 removed outlier: 4.172A pdb=" N LYS P 261 " --> pdb=" O GLY P 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 258 through 261' Processing helix chain 'P' and resid 262 through 276 removed outlier: 3.587A pdb=" N VAL P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 293 removed outlier: 3.649A pdb=" N ILE P 285 " --> pdb=" O LYS P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 310 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 330 through 344 Processing helix chain 'P' and resid 346 through 361 Processing helix chain 'P' and resid 364 through 378 Processing helix chain 'P' and resid 380 through 395 Processing helix chain 'P' and resid 398 through 412 Processing helix chain 'P' and resid 414 through 429 removed outlier: 3.823A pdb=" N CYS P 418 " --> pdb=" O MET P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 432 through 447 removed outlier: 3.622A pdb=" N LEU P 436 " --> pdb=" O ASP P 432 " (cutoff:3.500A) Processing helix chain 'P' and resid 448 through 463 Processing helix chain 'P' and resid 468 through 480 Processing helix chain 'P' and resid 483 through 500 Processing helix chain 'P' and resid 512 through 523 Processing helix chain 'P' and resid 525 through 538 removed outlier: 3.928A pdb=" N CYS P 532 " --> pdb=" O GLU P 528 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 Processing helix chain 'R' and resid 108 through 121 Processing helix chain 'S' and resid 20 through 26 Processing helix chain 'S' and resid 27 through 29 No H-bonds generated for 'chain 'S' and resid 27 through 29' Processing helix chain 'S' and resid 37 through 46 Processing helix chain 'S' and resid 50 through 70 Processing helix chain 'S' and resid 77 through 89 Processing helix chain 'S' and resid 97 through 109 Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'S' and resid 118 through 130 Processing helix chain 'S' and resid 135 through 146 Processing helix chain 'S' and resid 151 through 165 removed outlier: 4.301A pdb=" N TYR S 155 " --> pdb=" O LEU S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 181 Processing helix chain 'S' and resid 185 through 207 Processing helix chain 'S' and resid 303 through 307 Processing helix chain 'W' and resid 12 through 25 removed outlier: 4.144A pdb=" N GLU W 18 " --> pdb=" O ASP W 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 48 Processing helix chain 'X' and resid 49 through 67 Processing helix chain 'X' and resid 72 through 91 Processing helix chain 'X' and resid 92 through 110 Processing helix chain 'X' and resid 134 through 150 Processing helix chain 'X' and resid 151 through 162 removed outlier: 3.854A pdb=" N ALA X 155 " --> pdb=" O GLN X 151 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE X 162 " --> pdb=" O ILE X 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 183 Processing helix chain 'X' and resid 184 through 199 Processing helix chain 'X' and resid 202 through 213 Processing helix chain 'X' and resid 214 through 229 Processing helix chain 'X' and resid 235 through 248 Processing helix chain 'X' and resid 250 through 264 Processing helix chain 'X' and resid 270 through 285 Processing helix chain 'X' and resid 286 through 301 Processing helix chain 'X' and resid 304 through 319 removed outlier: 3.932A pdb=" N ASP X 309 " --> pdb=" O ILE X 305 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL X 310 " --> pdb=" O LYS X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 320 through 335 Processing helix chain 'X' and resid 338 through 353 removed outlier: 4.494A pdb=" N TRP X 342 " --> pdb=" O HIS X 338 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR X 351 " --> pdb=" O CYS X 347 " (cutoff:3.500A) Processing helix chain 'X' and resid 354 through 369 Processing helix chain 'X' and resid 372 through 387 Processing helix chain 'X' and resid 388 through 403 removed outlier: 3.682A pdb=" N HIS X 395 " --> pdb=" O GLU X 391 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE X 396 " --> pdb=" O ALA X 392 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG X 401 " --> pdb=" O ARG X 397 " (cutoff:3.500A) Processing helix chain 'X' and resid 406 through 421 Processing helix chain 'X' and resid 422 through 438 Processing helix chain 'X' and resid 441 through 454 removed outlier: 4.172A pdb=" N ASP X 454 " --> pdb=" O VAL X 450 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 472 removed outlier: 3.828A pdb=" N LEU X 464 " --> pdb=" O LYS X 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 490 removed outlier: 3.702A pdb=" N LEU X 485 " --> pdb=" O LYS X 481 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 505 removed outlier: 3.529A pdb=" N GLY X 495 " --> pdb=" O LYS X 491 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN X 501 " --> pdb=" O ALA X 497 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN X 505 " --> pdb=" O ASN X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 508 through 523 removed outlier: 3.844A pdb=" N HIS X 512 " --> pdb=" O ASP X 508 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA X 521 " --> pdb=" O ASP X 517 " (cutoff:3.500A) Processing helix chain 'X' and resid 524 through 539 Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 49 through 67 Processing helix chain 'Y' and resid 72 through 91 Processing helix chain 'Y' and resid 92 through 110 Processing helix chain 'Y' and resid 134 through 150 Processing helix chain 'Y' and resid 151 through 162 removed outlier: 3.522A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE Y 162 " --> pdb=" O ILE Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 183 Processing helix chain 'Y' and resid 184 through 199 removed outlier: 3.776A pdb=" N CYS Y 199 " --> pdb=" O VAL Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 213 Processing helix chain 'Y' and resid 214 through 229 Processing helix chain 'Y' and resid 235 through 249 removed outlier: 3.553A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 245 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 264 Processing helix chain 'Y' and resid 265 through 268 Processing helix chain 'Y' and resid 270 through 285 removed outlier: 3.597A pdb=" N GLY Y 275 " --> pdb=" O VAL Y 271 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 Processing helix chain 'Y' and resid 307 through 319 removed outlier: 3.850A pdb=" N TYR Y 311 " --> pdb=" O GLY Y 307 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR Y 313 " --> pdb=" O ASP Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 335 Processing helix chain 'Y' and resid 338 through 353 removed outlier: 4.358A pdb=" N TRP Y 342 " --> pdb=" O HIS Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 369 Processing helix chain 'Y' and resid 372 through 387 Processing helix chain 'Y' and resid 388 through 403 removed outlier: 4.032A pdb=" N ARG Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) Processing helix chain 'Y' and resid 406 through 421 Processing helix chain 'Y' and resid 422 through 437 Processing helix chain 'Y' and resid 441 through 453 Processing helix chain 'Y' and resid 457 through 472 removed outlier: 3.685A pdb=" N LEU Y 464 " --> pdb=" O LYS Y 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 490 Processing helix chain 'Y' and resid 492 through 504 removed outlier: 3.694A pdb=" N ASN Y 501 " --> pdb=" O ALA Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 508 through 523 removed outlier: 3.525A pdb=" N HIS Y 512 " --> pdb=" O ASP Y 508 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA Y 521 " --> pdb=" O ASP Y 517 " (cutoff:3.500A) Processing helix chain 'Y' and resid 524 through 539 Processing helix chain 'Y' and resid 542 through 551 removed outlier: 3.515A pdb=" N MET Y 549 " --> pdb=" O SER Y 545 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 35 Processing helix chain 'Z' and resid 39 through 41 No H-bonds generated for 'chain 'Z' and resid 39 through 41' Processing helix chain 'Z' and resid 58 through 78 Processing helix chain 'Z' and resid 108 through 113 removed outlier: 3.792A pdb=" N LYS Z 111 " --> pdb=" O LYS Z 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP Z 113 " --> pdb=" O ALA Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 138 Processing helix chain 'Z' and resid 139 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.910A pdb=" N ARG A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 596 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 78 removed outlier: 3.501A pdb=" N ARG A 77 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.790A pdb=" N LEU A 127 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 250 removed outlier: 6.486A pdb=" N MET A 257 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU A 249 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 255 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 268 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 430 through 433 removed outlier: 3.614A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 444 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER A 470 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLN A 458 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE A 468 " --> pdb=" O GLN A 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 478 through 482 removed outlier: 7.737A pdb=" N LEU A 497 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS A 508 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB1, first strand: chain 'A' and resid 1352 through 1353 removed outlier: 5.693A pdb=" N PHE L 135 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N ARG L 70 " --> pdb=" O ARG L 133 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N ARG L 133 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET L 136 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY L 99 " --> pdb=" O MET L 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER L 95 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS L 93 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN L 144 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG L 109 " --> pdb=" O VAL L 96 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL L 98 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU L 107 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1628 through 1629 removed outlier: 3.872A pdb=" N THR A1628 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A1620 " --> pdb=" O LEU A1697 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A1699 " --> pdb=" O VAL A1620 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL A1622 " --> pdb=" O VAL A1699 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1648 through 1652 removed outlier: 6.680A pdb=" N LEU A1633 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A1668 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A1675 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.837A pdb=" N PHE B 55 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 12 through 15 removed outlier: 5.844A pdb=" N VAL I 13 " --> pdb=" O GLU I 745 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU I 745 " --> pdb=" O VAL I 13 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 23 through 28 removed outlier: 3.737A pdb=" N ALA I 36 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL I 44 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER I 57 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU I 46 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 68 through 73 removed outlier: 4.568A pdb=" N CYS I 70 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU I 84 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS I 89 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS I 102 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP I 94 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER I 100 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 175 through 180 removed outlier: 3.775A pdb=" N GLY I 180 " --> pdb=" O PHE I 184 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE I 184 " --> pdb=" O GLY I 180 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA I 189 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS I 194 " --> pdb=" O ALA I 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 204 through 210 removed outlier: 6.249A pdb=" N CYS I 205 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU I 222 " --> pdb=" O CYS I 205 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA I 207 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER I 229 " --> pdb=" O ARG I 558 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG I 558 " --> pdb=" O SER I 229 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL I 231 " --> pdb=" O LEU I 556 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN I 235 " --> pdb=" O ILE I 552 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 574 through 578 removed outlier: 12.786A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 574 through 578 removed outlier: 12.786A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG I 703 " --> pdb=" O ILE I 616 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE I 618 " --> pdb=" O ARG I 703 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N MET I 705 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE I 620 " --> pdb=" O MET I 705 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE I 707 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N SER I 622 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 636 through 643 removed outlier: 6.051A pdb=" N CYS I 638 " --> pdb=" O LYS I 654 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS I 654 " --> pdb=" O CYS I 638 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP I 640 " --> pdb=" O VAL I 652 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL I 652 " --> pdb=" O ASP I 640 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG I 664 " --> pdb=" O LEU I 714 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 22 through 24 removed outlier: 3.579A pdb=" N GLN L 155 " --> pdb=" O TYR L 80 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR L 76 " --> pdb=" O TYR L 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AC6, first strand: chain 'N' and resid 647 through 648 Processing sheet with id=AC7, first strand: chain 'N' and resid 809 through 811 Processing sheet with id=AC8, first strand: chain 'Z' and resid 167 through 169 removed outlier: 3.606A pdb=" N ILE Z 155 " --> pdb=" O LEU Q 131 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU Q 133 " --> pdb=" O LEU Z 153 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU Z 153 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS Z 83 " --> pdb=" O TYR Z 156 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP Z 158 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL Z 81 " --> pdb=" O ASP Z 158 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN Z 82 " --> pdb=" O ILE Z 104 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN Z 90 " --> pdb=" O VAL Z 96 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL Z 96 " --> pdb=" O ASN Z 90 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU Z 97 " --> pdb=" O LYS Z 200 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS Z 191 " --> pdb=" O THR Z 187 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR Z 187 " --> pdb=" O HIS Z 191 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL Z 193 " --> pdb=" O SER Z 185 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER Z 185 " --> pdb=" O VAL Z 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER Z 195 " --> pdb=" O LEU Z 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 174 through 177 removed outlier: 3.661A pdb=" N ARG Q 174 " --> pdb=" O LEU Q 469 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR Q 466 " --> pdb=" O ALA Q 462 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA Q 462 " --> pdb=" O THR Q 466 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR Q 457 " --> pdb=" O MET Q 451 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N MET Q 451 " --> pdb=" O THR Q 457 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA Q 459 " --> pdb=" O LEU Q 449 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU Q 449 " --> pdb=" O ALA Q 459 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA Q 461 " --> pdb=" O LEU Q 447 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 190 through 192 Processing sheet with id=AD2, first strand: chain 'Q' and resid 229 through 234 removed outlier: 6.487A pdb=" N GLY Q 244 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL Q 232 " --> pdb=" O ALA Q 242 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA Q 242 " --> pdb=" O VAL Q 232 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP Q 234 " --> pdb=" O TYR Q 240 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR Q 240 " --> pdb=" O TRP Q 234 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU Q 249 " --> pdb=" O THR Q 245 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG Q 262 " --> pdb=" O LEU Q 252 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP Q 254 " --> pdb=" O ARG Q 260 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG Q 260 " --> pdb=" O ASP Q 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 271 through 277 removed outlier: 3.524A pdb=" N SER Q 273 " --> pdb=" O GLY Q 284 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU Q 281 " --> pdb=" O HIS Q 293 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N HIS Q 289 " --> pdb=" O SER Q 285 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA Q 303 " --> pdb=" O HIS Q 292 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP Q 294 " --> pdb=" O HIS Q 301 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS Q 301 " --> pdb=" O ASP Q 294 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 312 through 317 removed outlier: 3.694A pdb=" N GLN Q 349 " --> pdb=" O VAL Q 335 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 361 through 363 removed outlier: 3.708A pdb=" N SER Q 394 " --> pdb=" O ILE Q 384 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 402 through 408 removed outlier: 4.342A pdb=" N SER Q 404 " --> pdb=" O GLY Q 417 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER Q 408 " --> pdb=" O GLU Q 413 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU Q 413 " --> pdb=" O SER Q 408 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN Q 424 " --> pdb=" O HIS Q 418 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU Q 425 " --> pdb=" O GLU Q 438 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU Q 438 " --> pdb=" O LEU Q 425 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE Q 427 " --> pdb=" O VAL Q 436 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 446 through 451 removed outlier: 3.653A pdb=" N ALA R 462 " --> pdb=" O THR R 466 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR R 466 " --> pdb=" O ALA R 462 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA S 228 " --> pdb=" O ASP R 177 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 190 through 192 removed outlier: 3.582A pdb=" N LEU R 198 " --> pdb=" O TRP R 209 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP R 209 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 229 through 234 removed outlier: 6.191A pdb=" N GLY R 244 " --> pdb=" O SER R 230 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL R 232 " --> pdb=" O ALA R 242 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA R 242 " --> pdb=" O VAL R 232 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TRP R 234 " --> pdb=" O TYR R 240 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR R 240 " --> pdb=" O TRP R 234 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL R 243 " --> pdb=" O GLN R 251 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP R 254 " --> pdb=" O ARG R 260 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG R 260 " --> pdb=" O ASP R 254 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 273 through 276 removed outlier: 4.205A pdb=" N HIS R 292 " --> pdb=" O ALA R 303 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA R 303 " --> pdb=" O HIS R 292 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 314 through 317 removed outlier: 3.526A pdb=" N GLN R 349 " --> pdb=" O VAL R 335 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 358 through 363 removed outlier: 3.501A pdb=" N TRP R 385 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY R 375 " --> pdb=" O HIS R 381 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS R 381 " --> pdb=" O GLY R 375 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 402 through 408 removed outlier: 4.401A pdb=" N SER R 404 " --> pdb=" O GLY R 417 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY R 417 " --> pdb=" O SER R 404 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU R 425 " --> pdb=" O GLU R 438 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU R 438 " --> pdb=" O LEU R 425 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE R 427 " --> pdb=" O VAL R 436 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 43 through 48 4489 hydrogen bonds defined for protein. 13260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 34.70 Time building geometry restraints manager: 17.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 73214 1.57 - 1.92: 634 1.92 - 2.27: 0 2.27 - 2.62: 0 2.62 - 2.97: 1 Bond restraints: 73849 Sorted by residual: bond pdb=" C TRP N 92 " pdb=" N ASN N 93 " ideal model delta sigma weight residual 1.332 2.965 -1.633 1.40e-02 5.10e+03 1.36e+04 bond pdb=" C GLY A1278 " pdb=" N ARG A1279 " ideal model delta sigma weight residual 1.333 1.250 0.083 1.39e-02 5.18e+03 3.58e+01 bond pdb=" CA GLU K 330 " pdb=" CB GLU K 330 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.54e-02 4.22e+03 1.83e+01 bond pdb=" N SER H 566 " pdb=" CA SER H 566 " ideal model delta sigma weight residual 1.463 1.441 0.022 8.80e-03 1.29e+04 6.32e+00 bond pdb=" N ARG S 302 " pdb=" CA ARG S 302 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.24e-02 6.50e+03 5.66e+00 ... (remaining 73844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.66: 100074 15.66 - 31.32: 2 31.32 - 46.98: 1 46.98 - 62.64: 0 62.64 - 78.30: 1 Bond angle restraints: 100078 Sorted by residual: angle pdb=" O TRP N 92 " pdb=" C TRP N 92 " pdb=" N ASN N 93 " ideal model delta sigma weight residual 122.61 44.31 78.30 1.32e+00 5.74e-01 3.52e+03 angle pdb=" C TRP N 92 " pdb=" N ASN N 93 " pdb=" CA ASN N 93 " ideal model delta sigma weight residual 121.54 153.80 -32.26 1.91e+00 2.74e-01 2.85e+02 angle pdb=" C TYR N 125 " pdb=" N LEU N 126 " pdb=" CA LEU N 126 " ideal model delta sigma weight residual 121.70 140.45 -18.75 1.80e+00 3.09e-01 1.09e+02 angle pdb=" N ALA N 63 " pdb=" CA ALA N 63 " pdb=" C ALA N 63 " ideal model delta sigma weight residual 110.80 128.51 -17.71 2.13e+00 2.20e-01 6.92e+01 angle pdb=" CA TRP N 92 " pdb=" C TRP N 92 " pdb=" N ASN N 93 " ideal model delta sigma weight residual 114.90 105.01 9.89 1.37e+00 5.33e-01 5.21e+01 ... (remaining 100073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.70: 41893 25.70 - 51.41: 2287 51.41 - 77.11: 176 77.11 - 102.82: 49 102.82 - 128.52: 2 Dihedral angle restraints: 44407 sinusoidal: 17313 harmonic: 27094 Sorted by residual: dihedral pdb=" CA TRP B 14 " pdb=" C TRP B 14 " pdb=" N LEU B 15 " pdb=" CA LEU B 15 " ideal model delta harmonic sigma weight residual -180.00 -51.48 -128.52 0 5.00e+00 4.00e-02 6.61e+02 dihedral pdb=" CA TRP N 92 " pdb=" C TRP N 92 " pdb=" N ASN N 93 " pdb=" CA ASN N 93 " ideal model delta harmonic sigma weight residual 180.00 72.62 107.38 0 5.00e+00 4.00e-02 4.61e+02 dihedral pdb=" CA ILE J 220 " pdb=" C ILE J 220 " pdb=" N PRO J 221 " pdb=" CA PRO J 221 " ideal model delta harmonic sigma weight residual -180.00 -125.47 -54.53 0 5.00e+00 4.00e-02 1.19e+02 ... (remaining 44404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 10219 0.074 - 0.148: 985 0.148 - 0.221: 30 0.221 - 0.295: 1 0.295 - 0.369: 1 Chirality restraints: 11236 Sorted by residual: chirality pdb=" CA ALA N 63 " pdb=" N ALA N 63 " pdb=" C ALA N 63 " pdb=" CB ALA N 63 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA ALA N 64 " pdb=" N ALA N 64 " pdb=" C ALA N 64 " pdb=" CB ALA N 64 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE N 595 " pdb=" CA ILE N 595 " pdb=" CG1 ILE N 595 " pdb=" CG2 ILE N 595 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 11233 not shown) Planarity restraints: 12735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP N 92 " -0.135 2.00e-02 2.50e+03 2.39e-01 5.70e+02 pdb=" C TRP N 92 " 0.358 2.00e-02 2.50e+03 pdb=" O TRP N 92 " -0.280 2.00e-02 2.50e+03 pdb=" N ASN N 93 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR O 129 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C THR O 129 " 0.085 2.00e-02 2.50e+03 pdb=" O THR O 129 " -0.032 2.00e-02 2.50e+03 pdb=" N SER O 130 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS N 290 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C HIS N 290 " -0.080 2.00e-02 2.50e+03 pdb=" O HIS N 290 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS N 291 " 0.027 2.00e-02 2.50e+03 ... (remaining 12732 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1067 2.61 - 3.18: 71335 3.18 - 3.76: 120687 3.76 - 4.33: 162733 4.33 - 4.90: 256864 Nonbonded interactions: 612686 Sorted by model distance: nonbonded pdb=" OG SER C 267 " pdb=" OD1 ASN C 299 " model vdw 2.042 3.040 nonbonded pdb=" OH TYR F 73 " pdb=" O HIS H 18 " model vdw 2.061 3.040 nonbonded pdb=" O GLY R 321 " pdb=" OG SER R 338 " model vdw 2.067 3.040 nonbonded pdb=" O ASP G 15 " pdb=" OH TYR J 487 " model vdw 2.076 3.040 nonbonded pdb=" OG SER I 211 " pdb=" OG SER I 216 " model vdw 2.081 3.040 ... (remaining 612681 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 26 through 134 or resid 147 through 496 or (resid 497 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or r \ esid 498 through 500 or resid 511 through 538)) selection = chain 'P' } ncs_group { reference = chain 'F' selection = (chain 'H' and (resid 5 through 455 or (resid 456 through 459 and (name N or nam \ e CA or name C or name O or name CB )) or resid 460 through 767)) } ncs_group { reference = chain 'G' selection = chain 'W' } ncs_group { reference = (chain 'J' and (resid 2 through 93 or resid 127 through 213 or (resid 214 and (n \ ame N or name CA or name C or name O or name CB )) or resid 215 through 527)) selection = (chain 'K' and (resid 2 through 221 or (resid 222 and (name N or name CA or name \ C or name O or name CB )) or resid 223 through 346 or (resid 347 and (name N or \ name CA or name C or name O or name CB )) or resid 348 through 523 or (resid 52 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 525 through \ 527)) } ncs_group { reference = (chain 'Q' and (resid 128 or resid 134 or resid 139 or resid 141 through 142 or \ resid 145 or resid 149 or resid 154 through 156 or resid 159 or resid 162 or res \ id 165 through 476 or resid 492 through 499)) selection = (chain 'R' and (resid 86 or (resid 92 and (name N or name CA or name C or name O \ or name CB )) or (resid 99 and (name N or name CA or name C or name O or name C \ B )) or resid 101 through 102 or resid 105 or resid 109 or (resid 113 through 11 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 122 or resid \ 132 or resid 165 through 495 or (resid 496 and (name N or name CA or name C or \ name O or name CB )) or resid 497 through 499)) } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 36 through 540) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.340 Construct map_model_manager: 0.090 Extract box with map and model: 2.030 Check model and map are aligned: 0.420 Set scattering table: 0.520 Process input model: 132.710 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.410 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: 0.030 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 1.633 73849 Z= 0.590 Angle : 0.892 78.296 100078 Z= 0.529 Chirality : 0.043 0.369 11236 Planarity : 0.005 0.239 12735 Dihedral : 15.169 128.521 26840 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.54 % Favored : 91.25 % Rotamer: Outliers : 0.18 % Allowed : 7.49 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.31 % Twisted Proline : 0.87 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.08), residues: 9050 helix: -1.49 (0.06), residues: 5624 sheet: -1.93 (0.17), residues: 749 loop : -3.23 (0.11), residues: 2677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 970 HIS 0.012 0.001 HIS O 254 PHE 0.027 0.002 PHE L 177 TYR 0.023 0.002 TYR K 333 ARG 0.013 0.001 ARG Q 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18100 Ramachandran restraints generated. 9050 Oldfield, 0 Emsley, 9050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 892 time to evaluate : 6.334 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: 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 798 LYS cc_start: 0.8577 (tttt) cc_final: 0.8356 (mttt) REVERT: A 1070 LEU cc_start: 0.9504 (tp) cc_final: 0.9210 (tp) REVERT: A 1376 LEU cc_start: 0.8126 (tt) cc_final: 0.7918 (tt) REVERT: B 14 TRP cc_start: 0.4568 (OUTLIER) cc_final: 0.3366 (p-90) REVERT: B 28 MET cc_start: 0.4150 (tpt) cc_final: 0.2485 (mpp) REVERT: C 229 MET cc_start: 0.8326 (mmm) cc_final: 0.7686 (tpp) REVERT: C 484 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6861 (tp30) REVERT: C 519 TYR cc_start: 0.7241 (t80) cc_final: 0.6647 (t80) REVERT: E 101 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8019 (tm-30) REVERT: F 469 MET cc_start: 0.7840 (ttm) cc_final: 0.7612 (ttp) REVERT: F 516 MET cc_start: 0.7934 (mmm) cc_final: 0.7430 (tpp) REVERT: H 43 LEU cc_start: 0.8544 (tp) cc_final: 0.8151 (tp) REVERT: H 155 LEU cc_start: 0.8922 (tp) cc_final: 0.8661 (tt) REVERT: H 469 MET cc_start: 0.8933 (ttm) cc_final: 0.8659 (ttp) REVERT: H 516 MET cc_start: 0.8129 (mmm) cc_final: 0.7742 (mmt) REVERT: H 643 MET cc_start: 0.8425 (tpp) cc_final: 0.8193 (tpp) REVERT: I 283 MET cc_start: 0.5107 (tpp) cc_final: 0.4876 (tpp) REVERT: L 157 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7866 (mmtm) REVERT: M 2 ASP cc_start: 0.8177 (p0) cc_final: 0.7867 (p0) REVERT: M 60 LEU cc_start: 0.7825 (mt) cc_final: 0.7467 (mt) REVERT: N 185 MET cc_start: 0.6481 (mmm) cc_final: 0.6272 (mmp) REVERT: N 285 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8114 (m-10) REVERT: N 387 LEU cc_start: 0.8690 (mt) cc_final: 0.8352 (mp) REVERT: N 560 MET cc_start: 0.6181 (mmp) cc_final: 0.5572 (mmp) REVERT: N 564 MET cc_start: 0.5437 (mmt) cc_final: 0.4433 (tmm) REVERT: N 776 MET cc_start: 0.7446 (mtt) cc_final: 0.7214 (ptp) REVERT: O 239 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8067 (mm-30) REVERT: O 358 TYR cc_start: 0.6051 (p90) cc_final: 0.5827 (p90) REVERT: O 420 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8666 (mm) REVERT: O 437 MET cc_start: 0.8332 (mmm) cc_final: 0.7661 (mmm) REVERT: O 440 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8113 (tm-30) REVERT: O 646 MET cc_start: 0.7546 (mmp) cc_final: 0.7307 (ttt) REVERT: O 688 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8084 (mm-30) REVERT: O 735 MET cc_start: 0.7877 (ppp) cc_final: 0.7591 (mmp) REVERT: P 54 TRP cc_start: 0.7936 (t60) cc_final: 0.7686 (t60) REVERT: P 84 MET cc_start: 0.7692 (mmm) cc_final: 0.7214 (tpp) REVERT: P 208 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6526 (mm-30) REVERT: P 498 TYR cc_start: 0.6354 (m-80) cc_final: 0.5836 (t80) REVERT: Q 222 MET cc_start: 0.4101 (mmp) cc_final: 0.3863 (mmp) REVERT: Q 451 MET cc_start: 0.8344 (ttp) cc_final: 0.7896 (ttm) REVERT: R 241 LEU cc_start: 0.8520 (tp) cc_final: 0.8245 (tp) REVERT: R 433 MET cc_start: 0.6903 (mmm) cc_final: 0.6466 (mtm) REVERT: S 134 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7742 (mm-30) REVERT: S 139 TYR cc_start: 0.8794 (m-80) cc_final: 0.7750 (m-10) REVERT: X 60 LEU cc_start: 0.8514 (mt) cc_final: 0.8225 (tp) REVERT: X 304 LEU cc_start: 0.7457 (tp) cc_final: 0.7024 (tp) REVERT: X 529 MET cc_start: 0.3970 (mmt) cc_final: 0.3686 (mmm) REVERT: Y 173 MET cc_start: 0.8854 (tpt) cc_final: 0.7962 (tpt) REVERT: Y 295 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6844 (mt-10) REVERT: Y 429 MET cc_start: 0.8463 (mtm) cc_final: 0.8045 (mmm) REVERT: Y 549 MET cc_start: 0.7944 (mmt) cc_final: 0.7677 (mmm) REVERT: Z 23 PHE cc_start: 0.7803 (t80) cc_final: 0.7588 (t80) REVERT: Z 66 ASN cc_start: 0.7976 (t0) cc_final: 0.7337 (m-40) outliers start: 14 outliers final: 3 residues processed: 903 average time/residue: 0.8096 time to fit residues: 1223.4795 Evaluate side-chains 565 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 559 time to evaluate : 6.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain S residue 144 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 768 optimal weight: 8.9990 chunk 689 optimal weight: 7.9990 chunk 382 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 465 optimal weight: 6.9990 chunk 368 optimal weight: 9.9990 chunk 713 optimal weight: 10.0000 chunk 276 optimal weight: 0.9990 chunk 433 optimal weight: 2.9990 chunk 530 optimal weight: 1.9990 chunk 826 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 266 HIS A 411 HIS A 473 ASN A 601 ASN A 654 HIS A1068 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN A1247 HIS A1262 GLN A1266 HIS A1453 ASN ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS B 72 HIS C 82 GLN C 107 HIS C 202 HIS C 274 HIS C 347 HIS C 361 ASN C 386 GLN C 395 ASN C 518 GLN C 540 ASN F 103 HIS F 123 HIS ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 517 GLN F 545 HIS F 595 GLN H 123 HIS ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 HIS H 580 GLN H 595 GLN H 634 HIS H 648 GLN H 708 HIS H 716 ASN H 759 ASN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS I 323 ASN I 413 ASN I 455 HIS I 506 HIS J 16 GLN J 38 GLN J 58 HIS J 80 HIS J 271 HIS J 289 HIS J 318 HIS J 362 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 414 GLN J 453 HIS K 17 GLN K 58 HIS K 80 HIS K 244 ASN ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS K 362 GLN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 477 GLN L 65 ASN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 GLN N 239 GLN N 242 GLN N 266 HIS N 571 ASN N 639 HIS N 663 GLN ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 807 GLN ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN O 261 ASN ** O 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 342 HIS ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 412 HIS ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 472 HIS ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 722 HIS O 741 HIS P 148 ASN P 162 HIS P 211 ASN P 242 GLN P 287 ASN P 299 ASN P 305 ASN ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 427 GLN P 477 HIS P 495 GLN Q 183 ASN Q 292 HIS ** Q 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 181 GLN ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 GLN X 151 GLN X 177 ASN X 326 ASN X 338 HIS X 432 ASN X 523 ASN ** X 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 83 HIS Y 89 HIS Y 151 GLN ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 369 ASN Y 385 ASN ** Y 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 121 GLN Z 125 GLN Z 173 GLN Total number of N/Q/H flips: 105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 73849 Z= 0.244 Angle : 0.727 17.477 100078 Z= 0.377 Chirality : 0.043 0.363 11236 Planarity : 0.005 0.072 12735 Dihedral : 6.083 74.404 9985 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.42 % Favored : 92.50 % Rotamer: Outliers : 1.75 % Allowed : 12.88 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.58 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.08), residues: 9052 helix: -0.06 (0.07), residues: 5628 sheet: -1.57 (0.17), residues: 765 loop : -2.64 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 526 HIS 0.008 0.001 HIS F 18 PHE 0.058 0.002 PHE Z 24 TYR 0.028 0.002 TYR J 212 ARG 0.008 0.001 ARG R 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 711 time to evaluate : 6.302 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8558 (tpt) cc_final: 0.8067 (mmm) REVERT: A 1019 MET cc_start: 0.8033 (mmm) cc_final: 0.7456 (mtp) REVERT: A 1070 LEU cc_start: 0.9479 (tp) cc_final: 0.9200 (tp) REVERT: A 1078 MET cc_start: 0.8473 (mtm) cc_final: 0.8261 (mtm) REVERT: A 1191 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8341 (pt) REVERT: A 1373 MET cc_start: 0.7911 (mmm) cc_final: 0.7658 (mmm) REVERT: A 1609 LEU cc_start: 0.8773 (mm) cc_final: 0.8365 (mm) REVERT: A 1610 TYR cc_start: 0.8639 (p90) cc_final: 0.8367 (p90) REVERT: A 1652 MET cc_start: 0.8120 (tpp) cc_final: 0.6499 (ptp) REVERT: A 1786 MET cc_start: 0.7575 (mmm) cc_final: 0.7078 (mmm) REVERT: B 14 TRP cc_start: 0.4631 (OUTLIER) cc_final: 0.2889 (p-90) REVERT: B 28 MET cc_start: 0.3705 (tpt) cc_final: 0.2000 (mpp) REVERT: B 65 HIS cc_start: 0.2751 (OUTLIER) cc_final: 0.1790 (p-80) REVERT: C 229 MET cc_start: 0.8263 (mmm) cc_final: 0.7974 (tpp) REVERT: C 397 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7380 (mpp80) REVERT: C 484 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6559 (tp30) REVERT: E 101 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8033 (tm-30) REVERT: F 562 MET cc_start: 0.8705 (ppp) cc_final: 0.8498 (tmm) REVERT: H 43 LEU cc_start: 0.8617 (tp) cc_final: 0.8280 (tp) REVERT: H 469 MET cc_start: 0.8867 (ttm) cc_final: 0.8596 (ttp) REVERT: H 516 MET cc_start: 0.8015 (mmm) cc_final: 0.7623 (mmt) REVERT: H 588 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8634 (mppt) REVERT: I 27 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8393 (m) REVERT: I 92 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9006 (pp) REVERT: I 414 PHE cc_start: 0.5954 (m-10) cc_final: 0.5750 (m-10) REVERT: I 440 MET cc_start: 0.7805 (mmp) cc_final: 0.7173 (tmm) REVERT: J 358 PHE cc_start: 0.8212 (m-80) cc_final: 0.7979 (m-80) REVERT: K 354 MET cc_start: 0.7199 (tpp) cc_final: 0.6464 (mmm) REVERT: L 157 LYS cc_start: 0.7951 (mmtm) cc_final: 0.7543 (mmtm) REVERT: M 2 ASP cc_start: 0.8278 (p0) cc_final: 0.8043 (p0) REVERT: M 60 LEU cc_start: 0.7803 (mt) cc_final: 0.7393 (mt) REVERT: N 285 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8117 (m-10) REVERT: N 564 MET cc_start: 0.5067 (mmt) cc_final: 0.4209 (tmm) REVERT: N 772 ARG cc_start: 0.7510 (mpt90) cc_final: 0.6670 (mmm160) REVERT: O 239 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7976 (mm-30) REVERT: O 414 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6994 (pp) REVERT: O 420 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8736 (mm) REVERT: O 646 MET cc_start: 0.7396 (mmp) cc_final: 0.7157 (ttt) REVERT: O 688 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7937 (pt0) REVERT: O 735 MET cc_start: 0.7964 (ppp) cc_final: 0.7650 (mmp) REVERT: P 54 TRP cc_start: 0.7833 (t60) cc_final: 0.7488 (t60) REVERT: P 84 MET cc_start: 0.7582 (mmm) cc_final: 0.7202 (tpp) REVERT: P 124 LEU cc_start: 0.8881 (mt) cc_final: 0.8581 (mt) REVERT: P 243 LEU cc_start: 0.8395 (tp) cc_final: 0.7342 (tt) REVERT: P 286 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7859 (t80) REVERT: P 371 MET cc_start: 0.7550 (tpp) cc_final: 0.7338 (tpp) REVERT: P 435 MET cc_start: 0.8223 (mmm) cc_final: 0.7699 (mmm) REVERT: P 444 GLU cc_start: 0.8521 (tt0) cc_final: 0.8039 (tm-30) REVERT: P 498 TYR cc_start: 0.6036 (m-80) cc_final: 0.5819 (t80) REVERT: Q 222 MET cc_start: 0.4121 (mmp) cc_final: 0.3902 (mmp) REVERT: Q 451 MET cc_start: 0.8401 (ttp) cc_final: 0.8194 (ttm) REVERT: R 118 LEU cc_start: 0.8291 (mp) cc_final: 0.8029 (pp) REVERT: R 176 LEU cc_start: 0.8301 (mt) cc_final: 0.7950 (mt) REVERT: R 429 LYS cc_start: 0.8115 (tptt) cc_final: 0.7906 (mttt) REVERT: R 433 MET cc_start: 0.6670 (mmm) cc_final: 0.6282 (mtt) REVERT: S 134 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8046 (mm-30) REVERT: W 12 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7583 (ttpp) REVERT: X 304 LEU cc_start: 0.7337 (tp) cc_final: 0.7031 (tp) REVERT: X 529 MET cc_start: 0.3840 (mmt) cc_final: 0.3574 (mmm) REVERT: Y 173 MET cc_start: 0.8771 (tpt) cc_final: 0.8133 (tpt) REVERT: Y 369 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8268 (m-40) REVERT: Y 498 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5781 (tp) REVERT: Y 549 MET cc_start: 0.7881 (mmt) cc_final: 0.7450 (mmm) REVERT: Z 66 ASN cc_start: 0.7957 (t0) cc_final: 0.7273 (m-40) outliers start: 133 outliers final: 58 residues processed: 807 average time/residue: 0.7161 time to fit residues: 1003.2955 Evaluate side-chains 624 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 553 time to evaluate : 6.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 65 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 314 HIS Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 293 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 476 LEU Chi-restraints excluded: chain O residue 514 ILE Chi-restraints excluded: chain O residue 612 LYS Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain S residue 125 TRP Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain X residue 413 LEU Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 369 ASN Chi-restraints excluded: chain Y residue 498 LEU Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Z residue 194 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 459 optimal weight: 0.7980 chunk 256 optimal weight: 6.9990 chunk 687 optimal weight: 20.0000 chunk 562 optimal weight: 30.0000 chunk 227 optimal weight: 5.9990 chunk 827 optimal weight: 20.0000 chunk 894 optimal weight: 6.9990 chunk 737 optimal weight: 5.9990 chunk 820 optimal weight: 20.0000 chunk 282 optimal weight: 2.9990 chunk 664 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS C 107 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN H 166 GLN ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 502 GLN ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS K 316 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 702 GLN N 726 ASN N 759 GLN ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 477 HIS ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 202 HIS ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 401 GLN ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 198 GLN X 395 HIS X 471 GLN ** X 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 73849 Z= 0.312 Angle : 0.734 17.060 100078 Z= 0.380 Chirality : 0.044 0.353 11236 Planarity : 0.005 0.072 12735 Dihedral : 5.986 70.827 9983 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.70 % Favored : 92.23 % Rotamer: Outliers : 2.36 % Allowed : 15.73 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.58 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.09), residues: 9052 helix: 0.32 (0.07), residues: 5636 sheet: -1.49 (0.17), residues: 769 loop : -2.51 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1386 HIS 0.019 0.001 HIS B 65 PHE 0.037 0.002 PHE Y 294 TYR 0.038 0.002 TYR J 212 ARG 0.008 0.001 ARG R 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 583 time to evaluate : 6.434 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: A 257 MET cc_start: 0.8584 (tpt) cc_final: 0.8079 (mmm) REVERT: A 637 MET cc_start: 0.8996 (tmm) cc_final: 0.8757 (tmm) REVERT: A 653 TYR cc_start: 0.5062 (t80) cc_final: 0.4631 (t80) REVERT: A 1070 LEU cc_start: 0.9496 (tp) cc_final: 0.9223 (tp) REVERT: A 1191 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8518 (pt) REVERT: A 1228 LEU cc_start: 0.8334 (mt) cc_final: 0.8121 (mp) REVERT: A 1786 MET cc_start: 0.7497 (mmm) cc_final: 0.6903 (mmm) REVERT: B 14 TRP cc_start: 0.4860 (OUTLIER) cc_final: 0.3150 (p-90) REVERT: B 28 MET cc_start: 0.3992 (tpt) cc_final: 0.2241 (mpp) REVERT: B 61 LEU cc_start: 0.4134 (OUTLIER) cc_final: 0.3334 (mt) REVERT: C 229 MET cc_start: 0.8280 (mmm) cc_final: 0.7746 (tpp) REVERT: C 397 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7572 (mpp80) REVERT: C 484 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6609 (tp30) REVERT: E 79 MET cc_start: 0.8672 (mmm) cc_final: 0.8212 (mmm) REVERT: E 101 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8088 (tm-30) REVERT: F 562 MET cc_start: 0.8783 (ppp) cc_final: 0.8506 (tmm) REVERT: F 628 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7168 (mm) REVERT: H 43 LEU cc_start: 0.8596 (tp) cc_final: 0.8221 (tp) REVERT: H 155 LEU cc_start: 0.8870 (mt) cc_final: 0.8602 (mt) REVERT: H 463 MET cc_start: 0.9168 (tpp) cc_final: 0.8817 (tpp) REVERT: H 469 MET cc_start: 0.8941 (ttm) cc_final: 0.8657 (ttp) REVERT: H 516 MET cc_start: 0.8063 (mmm) cc_final: 0.7642 (mmt) REVERT: H 588 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8610 (mppt) REVERT: I 283 MET cc_start: 0.4728 (tpp) cc_final: 0.4160 (tpp) REVERT: I 363 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8877 (mm) REVERT: I 414 PHE cc_start: 0.6084 (m-80) cc_final: 0.5797 (m-10) REVERT: I 422 TYR cc_start: 0.8080 (t80) cc_final: 0.7879 (t80) REVERT: J 170 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8272 (pt) REVERT: J 378 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7900 (m-10) REVERT: L 136 MET cc_start: 0.8378 (ptm) cc_final: 0.8162 (ptm) REVERT: N 285 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8224 (m-10) REVERT: N 399 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8463 (tt) REVERT: N 564 MET cc_start: 0.5010 (mmt) cc_final: 0.4242 (tmm) REVERT: N 696 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5877 (tpp) REVERT: O 239 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8104 (mm-30) REVERT: O 414 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6753 (pp) REVERT: O 420 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8836 (mm) REVERT: O 444 MET cc_start: 0.8901 (mmm) cc_final: 0.8592 (tpp) REVERT: O 646 MET cc_start: 0.7452 (mmp) cc_final: 0.7214 (ttt) REVERT: O 688 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7977 (pt0) REVERT: O 735 MET cc_start: 0.8099 (ppp) cc_final: 0.7723 (mmp) REVERT: P 54 TRP cc_start: 0.8078 (t60) cc_final: 0.7676 (t60) REVERT: P 84 MET cc_start: 0.7598 (mmm) cc_final: 0.7233 (tpp) REVERT: P 243 LEU cc_start: 0.8681 (tp) cc_final: 0.8332 (tp) REVERT: P 286 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7852 (t80) REVERT: P 371 MET cc_start: 0.7677 (tpp) cc_final: 0.7399 (tpp) REVERT: P 435 MET cc_start: 0.8244 (mmm) cc_final: 0.7666 (mmm) REVERT: P 444 GLU cc_start: 0.8584 (tt0) cc_final: 0.8033 (tm-30) REVERT: P 498 TYR cc_start: 0.6131 (m-80) cc_final: 0.5860 (t80) REVERT: Q 222 MET cc_start: 0.3929 (mmp) cc_final: 0.3693 (mmp) REVERT: Q 451 MET cc_start: 0.8423 (ttp) cc_final: 0.8202 (ttm) REVERT: R 240 TYR cc_start: 0.7884 (m-10) cc_final: 0.7660 (m-10) REVERT: R 433 MET cc_start: 0.6596 (mmm) cc_final: 0.5971 (mtm) REVERT: S 134 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7764 (mm-30) REVERT: S 139 TYR cc_start: 0.8550 (m-80) cc_final: 0.7695 (m-80) REVERT: S 170 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7911 (mmtm) REVERT: X 304 LEU cc_start: 0.7568 (tp) cc_final: 0.7115 (tp) REVERT: X 529 MET cc_start: 0.3845 (mmt) cc_final: 0.3534 (mmm) REVERT: Y 173 MET cc_start: 0.8729 (tpt) cc_final: 0.7792 (tpt) REVERT: Y 294 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6741 (t80) REVERT: Y 368 LEU cc_start: 0.9172 (mp) cc_final: 0.8970 (tp) REVERT: Y 498 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5806 (tp) REVERT: Y 549 MET cc_start: 0.7929 (mmt) cc_final: 0.7690 (mmp) REVERT: Z 38 TYR cc_start: 0.7500 (t80) cc_final: 0.7291 (t80) outliers start: 179 outliers final: 101 residues processed: 719 average time/residue: 0.6627 time to fit residues: 841.6331 Evaluate side-chains 635 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 517 time to evaluate : 6.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1794 ASP Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 564 LYS Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain H residue 678 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 209 LEU Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 378 TYR Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 79 CYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 293 ASP Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 177 PHE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 557 CYS Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 696 MET Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 476 LEU Chi-restraints excluded: chain O residue 514 ILE Chi-restraints excluded: chain O residue 599 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 612 LYS Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain S residue 125 TRP Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain X residue 63 MET Chi-restraints excluded: chain X residue 239 TRP Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 413 LEU Chi-restraints excluded: chain Y residue 294 PHE Chi-restraints excluded: chain Y residue 334 ILE Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 498 LEU Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Z residue 194 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 817 optimal weight: 9.9990 chunk 622 optimal weight: 9.9990 chunk 429 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 395 optimal weight: 5.9990 chunk 555 optimal weight: 20.0000 chunk 830 optimal weight: 7.9990 chunk 879 optimal weight: 20.0000 chunk 434 optimal weight: 2.9990 chunk 787 optimal weight: 30.0000 chunk 237 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1429 ASN ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS C 107 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN I 114 HIS ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 382 GLN ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 552 GLN ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 HIS X 385 ASN ** X 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 73849 Z= 0.347 Angle : 0.750 16.863 100078 Z= 0.386 Chirality : 0.044 0.349 11236 Planarity : 0.005 0.072 12735 Dihedral : 5.993 72.046 9983 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.79 % Favored : 92.15 % Rotamer: Outliers : 3.37 % Allowed : 17.18 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.58 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.09), residues: 9052 helix: 0.45 (0.07), residues: 5637 sheet: -1.44 (0.17), residues: 766 loop : -2.45 (0.12), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1386 HIS 0.013 0.001 HIS B 65 PHE 0.038 0.002 PHE I 25 TYR 0.029 0.002 TYR Q 144 ARG 0.015 0.001 ARG H 625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 541 time to evaluate : 7.867 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: A 257 MET cc_start: 0.8605 (tpt) cc_final: 0.8092 (mmm) REVERT: A 637 MET cc_start: 0.8999 (tmm) cc_final: 0.8764 (tmm) REVERT: A 1019 MET cc_start: 0.7677 (mtp) cc_final: 0.7265 (mtp) REVERT: A 1070 LEU cc_start: 0.9505 (tp) cc_final: 0.9209 (tp) REVERT: A 1107 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8351 (pp) REVERT: A 1191 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8605 (pt) REVERT: A 1786 MET cc_start: 0.7510 (mmm) cc_final: 0.7027 (mmm) REVERT: B 14 TRP cc_start: 0.5577 (OUTLIER) cc_final: 0.3575 (p-90) REVERT: B 28 MET cc_start: 0.4056 (tpt) cc_final: 0.2227 (mpp) REVERT: C 364 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7395 (t80) REVERT: C 397 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7396 (mpp80) REVERT: C 484 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6608 (tp30) REVERT: F 562 MET cc_start: 0.8772 (ppp) cc_final: 0.8526 (ppp) REVERT: F 628 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7145 (mm) REVERT: H 43 LEU cc_start: 0.8640 (tp) cc_final: 0.8259 (tp) REVERT: H 155 LEU cc_start: 0.8883 (mt) cc_final: 0.8634 (mt) REVERT: H 463 MET cc_start: 0.9201 (tpp) cc_final: 0.8874 (tpp) REVERT: H 469 MET cc_start: 0.8964 (ttm) cc_final: 0.8657 (ttp) REVERT: H 516 MET cc_start: 0.8079 (mmm) cc_final: 0.7680 (mmt) REVERT: H 588 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8647 (mppt) REVERT: I 27 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8464 (m) REVERT: I 414 PHE cc_start: 0.6225 (m-80) cc_final: 0.6001 (m-10) REVERT: I 548 MET cc_start: 0.6374 (mmm) cc_final: 0.6125 (mmm) REVERT: J 314 HIS cc_start: 0.6597 (t-90) cc_final: 0.6375 (t-170) REVERT: J 378 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7979 (m-10) REVERT: K 258 MET cc_start: 0.8166 (tpp) cc_final: 0.7408 (tpp) REVERT: N 285 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: N 290 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.5859 (m170) REVERT: N 399 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8480 (tt) REVERT: N 564 MET cc_start: 0.5335 (mmt) cc_final: 0.4234 (tmm) REVERT: O 239 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8016 (mm-30) REVERT: O 414 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6736 (pp) REVERT: O 420 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8860 (mm) REVERT: O 460 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6971 (tp-100) REVERT: O 646 MET cc_start: 0.7430 (mmp) cc_final: 0.7158 (ttt) REVERT: O 735 MET cc_start: 0.8119 (ppp) cc_final: 0.7710 (mmp) REVERT: P 54 TRP cc_start: 0.8144 (t60) cc_final: 0.7776 (t60) REVERT: P 84 MET cc_start: 0.7588 (mmm) cc_final: 0.7249 (tpp) REVERT: P 286 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7825 (t80) REVERT: P 312 MET cc_start: 0.7393 (mtp) cc_final: 0.7172 (ttp) REVERT: P 435 MET cc_start: 0.8218 (mmm) cc_final: 0.7607 (mmm) REVERT: P 498 TYR cc_start: 0.6405 (m-80) cc_final: 0.6040 (t80) REVERT: Q 222 MET cc_start: 0.3908 (mmp) cc_final: 0.3690 (mmp) REVERT: Q 451 MET cc_start: 0.8374 (ttp) cc_final: 0.7947 (ttt) REVERT: R 176 LEU cc_start: 0.8198 (mp) cc_final: 0.7906 (mt) REVERT: R 240 TYR cc_start: 0.8067 (m-10) cc_final: 0.7782 (m-10) REVERT: R 316 ARG cc_start: 0.8600 (ttm110) cc_final: 0.8133 (ttm110) REVERT: S 134 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7737 (mm-30) REVERT: S 139 TYR cc_start: 0.8552 (m-80) cc_final: 0.7682 (m-80) REVERT: S 170 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7866 (mmtt) REVERT: X 132 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7582 (pt) REVERT: X 271 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8898 (t) REVERT: X 304 LEU cc_start: 0.7344 (tp) cc_final: 0.6877 (tp) REVERT: X 529 MET cc_start: 0.3858 (mmt) cc_final: 0.3524 (mmm) REVERT: Y 142 MET cc_start: 0.8315 (mmm) cc_final: 0.8055 (mmm) REVERT: Y 173 MET cc_start: 0.8781 (tpt) cc_final: 0.7856 (tpt) REVERT: Y 294 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6856 (t80) REVERT: Y 498 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5800 (tp) outliers start: 256 outliers final: 152 residues processed: 744 average time/residue: 0.6655 time to fit residues: 880.5496 Evaluate side-chains 672 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 500 time to evaluate : 6.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1581 ILE Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 564 LYS Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 562 MET Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain H residue 678 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 643 PHE Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 209 LEU Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 230 ASN Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 289 HIS Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 378 TYR Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 79 CYS Chi-restraints excluded: chain K residue 135 LEU Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 293 ASP Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 177 PHE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 277 CYS Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain N residue 290 HIS Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 557 CYS Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 112 PHE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 460 GLN Chi-restraints excluded: chain O residue 476 LEU Chi-restraints excluded: chain O residue 514 ILE Chi-restraints excluded: chain O residue 599 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 612 LYS Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 259 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 333 VAL Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain S residue 125 TRP Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 221 VAL Chi-restraints excluded: chain X residue 63 MET Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain X residue 239 TRP Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 356 SER Chi-restraints excluded: chain X residue 413 LEU Chi-restraints excluded: chain Y residue 148 MET Chi-restraints excluded: chain Y residue 294 PHE Chi-restraints excluded: chain Y residue 334 ILE Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 498 LEU Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Z residue 194 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 732 optimal weight: 20.0000 chunk 499 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 654 optimal weight: 0.8980 chunk 362 optimal weight: 7.9990 chunk 750 optimal weight: 10.0000 chunk 608 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 449 optimal weight: 7.9990 chunk 789 optimal weight: 0.0670 chunk 221 optimal weight: 8.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1429 ASN ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 HIS ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 GLN ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 341 GLN ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 202 HIS P 252 GLN ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 HIS Q 323 HIS ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 298 GLN ** X 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 458 GLN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 73849 Z= 0.195 Angle : 0.668 16.591 100078 Z= 0.342 Chirality : 0.042 0.347 11236 Planarity : 0.004 0.072 12735 Dihedral : 5.702 74.761 9982 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 2.57 % Allowed : 18.88 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.87 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.09), residues: 9052 helix: 0.81 (0.07), residues: 5657 sheet: -1.24 (0.18), residues: 766 loop : -2.31 (0.12), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1386 HIS 0.007 0.001 HIS X 89 PHE 0.043 0.002 PHE I 25 TYR 0.022 0.001 TYR A 653 ARG 0.008 0.000 ARG O 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 626 time to evaluate : 6.374 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8524 (tpt) cc_final: 0.8176 (mmm) REVERT: A 1019 MET cc_start: 0.7776 (mtp) cc_final: 0.7529 (mtp) REVERT: A 1070 LEU cc_start: 0.9460 (tp) cc_final: 0.9184 (tp) REVERT: A 1107 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8377 (pp) REVERT: A 1191 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8429 (pt) REVERT: A 1786 MET cc_start: 0.7612 (mmm) cc_final: 0.7125 (mmm) REVERT: B 28 MET cc_start: 0.3345 (tpt) cc_final: 0.1617 (mpp) REVERT: C 168 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6926 (t0) REVERT: C 364 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7455 (t80) REVERT: C 397 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6996 (mpp80) REVERT: C 484 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6498 (tp30) REVERT: E 101 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8026 (tm-30) REVERT: F 516 MET cc_start: 0.7832 (mmm) cc_final: 0.7455 (tpp) REVERT: F 562 MET cc_start: 0.8706 (ppp) cc_final: 0.8423 (ppp) REVERT: H 43 LEU cc_start: 0.8537 (tp) cc_final: 0.8235 (tp) REVERT: H 463 MET cc_start: 0.9138 (tpp) cc_final: 0.8742 (tpp) REVERT: H 469 MET cc_start: 0.8884 (ttm) cc_final: 0.8531 (ttp) REVERT: H 516 MET cc_start: 0.7836 (mmm) cc_final: 0.7476 (mmt) REVERT: H 588 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8483 (mppt) REVERT: I 27 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8513 (m) REVERT: I 330 LEU cc_start: 0.7881 (tt) cc_final: 0.7645 (pp) REVERT: I 414 PHE cc_start: 0.6463 (m-80) cc_final: 0.6185 (m-10) REVERT: J 283 GLU cc_start: 0.8036 (tp30) cc_final: 0.7783 (tm-30) REVERT: J 358 PHE cc_start: 0.8118 (m-80) cc_final: 0.7856 (m-10) REVERT: K 167 PHE cc_start: 0.7753 (t80) cc_final: 0.7313 (t80) REVERT: K 258 MET cc_start: 0.7929 (tpp) cc_final: 0.7443 (tpp) REVERT: K 374 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6414 (mt) REVERT: L 128 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.4703 (m-70) REVERT: N 277 CYS cc_start: 0.7047 (p) cc_final: 0.6683 (p) REVERT: N 285 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: N 399 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8426 (tt) REVERT: N 564 MET cc_start: 0.5257 (mmt) cc_final: 0.4190 (tmm) REVERT: O 112 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8029 (t80) REVERT: O 113 ASP cc_start: 0.8350 (m-30) cc_final: 0.7991 (p0) REVERT: O 139 MET cc_start: 0.6970 (mmp) cc_final: 0.6248 (mmp) REVERT: O 239 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7910 (mm-30) REVERT: O 420 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8741 (mm) REVERT: O 444 MET cc_start: 0.9040 (mmm) cc_final: 0.8751 (tpp) REVERT: O 448 MET cc_start: 0.6856 (tmm) cc_final: 0.6652 (tmm) REVERT: O 460 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6776 (tp-100) REVERT: O 646 MET cc_start: 0.7265 (mmp) cc_final: 0.7044 (ttt) REVERT: O 688 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7889 (pt0) REVERT: O 735 MET cc_start: 0.8124 (ppp) cc_final: 0.7688 (mmp) REVERT: P 54 TRP cc_start: 0.7960 (t60) cc_final: 0.7657 (t60) REVERT: P 84 MET cc_start: 0.7541 (mmm) cc_final: 0.7203 (tpp) REVERT: P 286 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7616 (t80) REVERT: P 371 MET cc_start: 0.7673 (tpp) cc_final: 0.7424 (tpp) REVERT: P 435 MET cc_start: 0.8076 (mmm) cc_final: 0.7778 (mtt) REVERT: P 444 GLU cc_start: 0.8605 (tt0) cc_final: 0.7993 (tm-30) REVERT: Q 451 MET cc_start: 0.8433 (ttp) cc_final: 0.8200 (ttm) REVERT: R 176 LEU cc_start: 0.8119 (mp) cc_final: 0.7891 (mt) REVERT: R 316 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8409 (ttm110) REVERT: S 134 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7679 (mm-30) REVERT: S 138 MET cc_start: 0.7887 (tpp) cc_final: 0.7639 (tpp) REVERT: S 170 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7903 (mmtt) REVERT: W 5 LYS cc_start: 0.7472 (mmtt) cc_final: 0.6878 (mmmt) REVERT: X 271 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8892 (t) REVERT: X 529 MET cc_start: 0.3773 (mmt) cc_final: 0.3452 (mmm) REVERT: Y 142 MET cc_start: 0.8106 (mmm) cc_final: 0.7716 (mmm) REVERT: Y 173 MET cc_start: 0.8613 (tpt) cc_final: 0.7717 (tpt) outliers start: 195 outliers final: 102 residues processed: 778 average time/residue: 0.6573 time to fit residues: 900.7660 Evaluate side-chains 648 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 530 time to evaluate : 6.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1016 MET Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 601 LEU Chi-restraints excluded: chain I residue 643 PHE Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 209 LEU Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 79 CYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 293 ASP Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 128 HIS Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 557 CYS Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 112 PHE Chi-restraints excluded: chain O residue 417 LEU Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 460 GLN Chi-restraints excluded: chain O residue 476 LEU Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 514 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 612 LYS Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain Q residue 259 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 333 VAL Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain S residue 221 VAL Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 239 TRP Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 356 SER Chi-restraints excluded: chain X residue 413 LEU Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 295 optimal weight: 6.9990 chunk 792 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 516 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 880 optimal weight: 7.9990 chunk 730 optimal weight: 5.9990 chunk 407 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 291 optimal weight: 0.6980 chunk 462 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 HIS A1429 ASN ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1646 GLN C 107 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 ASN K 383 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 HIS ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 GLN ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73849 Z= 0.198 Angle : 0.677 16.442 100078 Z= 0.343 Chirality : 0.041 0.343 11236 Planarity : 0.004 0.072 12735 Dihedral : 5.562 74.978 9982 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 2.87 % Allowed : 19.61 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.87 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.09), residues: 9052 helix: 0.92 (0.07), residues: 5690 sheet: -1.11 (0.18), residues: 756 loop : -2.25 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP N 299 HIS 0.008 0.001 HIS X 89 PHE 0.048 0.002 PHE I 25 TYR 0.029 0.001 TYR A1610 ARG 0.010 0.000 ARG Y 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 599 time to evaluate : 6.360 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 257 MET cc_start: 0.8522 (tpt) cc_final: 0.8175 (mmm) REVERT: A 667 MET cc_start: 0.6309 (tmm) cc_final: 0.6089 (tmm) REVERT: A 1070 LEU cc_start: 0.9465 (tp) cc_final: 0.9160 (tp) REVERT: A 1191 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8271 (pt) REVERT: A 1786 MET cc_start: 0.7633 (mmm) cc_final: 0.7227 (mmm) REVERT: B 28 MET cc_start: 0.3352 (tpt) cc_final: 0.1723 (mpp) REVERT: C 364 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7451 (t80) REVERT: C 397 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6996 (mpp80) REVERT: C 484 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6503 (tp30) REVERT: E 101 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8020 (tm-30) REVERT: F 516 MET cc_start: 0.7764 (mmm) cc_final: 0.7236 (tpp) REVERT: F 536 MET cc_start: 0.8564 (mmt) cc_final: 0.8344 (mmt) REVERT: F 562 MET cc_start: 0.8698 (ppp) cc_final: 0.8408 (ppp) REVERT: H 43 LEU cc_start: 0.8461 (tp) cc_final: 0.8182 (tp) REVERT: H 463 MET cc_start: 0.9135 (tpp) cc_final: 0.8656 (tpp) REVERT: H 469 MET cc_start: 0.8886 (ttm) cc_final: 0.8541 (ttp) REVERT: H 516 MET cc_start: 0.7783 (mmm) cc_final: 0.7507 (mmt) REVERT: H 588 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8693 (mtmm) REVERT: H 738 LEU cc_start: 0.8234 (tp) cc_final: 0.7964 (tp) REVERT: I 27 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8426 (m) REVERT: I 283 MET cc_start: 0.4719 (tpp) cc_final: 0.4155 (tpp) REVERT: I 330 LEU cc_start: 0.7888 (tt) cc_final: 0.7606 (pp) REVERT: J 283 GLU cc_start: 0.8092 (tp30) cc_final: 0.7801 (tm-30) REVERT: J 358 PHE cc_start: 0.8090 (m-80) cc_final: 0.7809 (m-10) REVERT: K 205 PHE cc_start: 0.7959 (m-80) cc_final: 0.7659 (m-80) REVERT: K 258 MET cc_start: 0.7937 (tpp) cc_final: 0.7481 (tpp) REVERT: N 277 CYS cc_start: 0.7106 (p) cc_final: 0.6728 (p) REVERT: N 285 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7904 (m-10) REVERT: N 290 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.5758 (m170) REVERT: N 399 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8428 (tt) REVERT: N 418 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8066 (tm-30) REVERT: N 564 MET cc_start: 0.5193 (mmt) cc_final: 0.4106 (tmm) REVERT: N 772 ARG cc_start: 0.7341 (mpt90) cc_final: 0.6659 (mmm160) REVERT: O 112 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.8011 (t80) REVERT: O 139 MET cc_start: 0.6950 (mmp) cc_final: 0.6370 (mmp) REVERT: O 239 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7577 (tp30) REVERT: O 444 MET cc_start: 0.8966 (mmm) cc_final: 0.8742 (tpp) REVERT: O 460 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6748 (tp-100) REVERT: O 646 MET cc_start: 0.7321 (mmp) cc_final: 0.7090 (ttt) REVERT: O 735 MET cc_start: 0.8268 (ppp) cc_final: 0.7708 (mmp) REVERT: P 54 TRP cc_start: 0.8034 (t60) cc_final: 0.7795 (t60) REVERT: P 84 MET cc_start: 0.7555 (mmm) cc_final: 0.7215 (tpp) REVERT: P 286 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7584 (t80) REVERT: P 371 MET cc_start: 0.7684 (tpp) cc_final: 0.7367 (tpp) REVERT: P 435 MET cc_start: 0.8072 (mmm) cc_final: 0.7794 (mtt) REVERT: P 444 GLU cc_start: 0.8570 (tt0) cc_final: 0.7962 (tm-30) REVERT: Q 451 MET cc_start: 0.8457 (ttp) cc_final: 0.8088 (ttm) REVERT: R 118 LEU cc_start: 0.7936 (mt) cc_final: 0.7526 (pp) REVERT: R 176 LEU cc_start: 0.8149 (mp) cc_final: 0.7894 (mt) REVERT: R 240 TYR cc_start: 0.7360 (m-10) cc_final: 0.7131 (m-10) REVERT: S 134 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7632 (mm-30) REVERT: S 138 MET cc_start: 0.8291 (tpp) cc_final: 0.8003 (tpp) REVERT: S 139 TYR cc_start: 0.8566 (m-80) cc_final: 0.7736 (m-80) REVERT: S 170 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7998 (mmtt) REVERT: X 304 LEU cc_start: 0.7737 (tp) cc_final: 0.7338 (tp) REVERT: X 397 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7750 (mtm180) REVERT: X 529 MET cc_start: 0.3565 (mmt) cc_final: 0.3290 (mmm) REVERT: Y 142 MET cc_start: 0.8235 (mmm) cc_final: 0.7203 (mmm) REVERT: Y 173 MET cc_start: 0.8596 (tpt) cc_final: 0.7685 (tpt) REVERT: Y 294 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.6541 (t80) REVERT: Y 498 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5747 (tp) outliers start: 218 outliers final: 133 residues processed: 776 average time/residue: 0.6498 time to fit residues: 889.4098 Evaluate side-chains 664 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 518 time to evaluate : 6.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1373 MET Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1581 ILE Chi-restraints excluded: chain A residue 1646 GLN Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 643 PHE Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 209 LEU Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 79 CYS Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 293 ASP Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain N residue 290 HIS Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 557 CYS Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 112 PHE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 460 GLN Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 508 MET Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 612 LYS Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 409 TYR Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 259 LYS Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 333 VAL Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 221 VAL Chi-restraints excluded: chain X residue 44 MET Chi-restraints excluded: chain X residue 63 MET Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 239 TRP Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 413 LEU Chi-restraints excluded: chain Y residue 199 CYS Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 294 PHE Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 498 LEU Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 848 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 501 optimal weight: 0.0870 chunk 642 optimal weight: 8.9990 chunk 498 optimal weight: 5.9990 chunk 741 optimal weight: 30.0000 chunk 491 optimal weight: 8.9990 chunk 877 optimal weight: 0.8980 chunk 548 optimal weight: 8.9990 chunk 534 optimal weight: 0.9980 chunk 404 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1429 ASN ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS C 236 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 HIS K 264 HIS ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 370 HIS ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 460 GLN ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 361 ASN Q 323 HIS ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 73849 Z= 0.180 Angle : 0.669 16.405 100078 Z= 0.338 Chirality : 0.041 0.342 11236 Planarity : 0.004 0.071 12735 Dihedral : 5.440 75.376 9980 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.23 % Favored : 93.75 % Rotamer: Outliers : 2.69 % Allowed : 20.09 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.58 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.09), residues: 9052 helix: 1.03 (0.07), residues: 5681 sheet: -0.94 (0.18), residues: 751 loop : -2.20 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 526 HIS 0.009 0.001 HIS J 318 PHE 0.040 0.001 PHE J 164 TYR 0.057 0.001 TYR K 378 ARG 0.009 0.000 ARG Y 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 622 time to evaluate : 6.591 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 74 TRP cc_start: 0.8813 (p90) cc_final: 0.8556 (p90) REVERT: A 257 MET cc_start: 0.8456 (tpt) cc_final: 0.8217 (mmm) REVERT: A 1070 LEU cc_start: 0.9444 (tp) cc_final: 0.9143 (tp) REVERT: A 1191 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8153 (pt) REVERT: A 1544 MET cc_start: 0.8130 (mmm) cc_final: 0.7918 (mmm) REVERT: A 1786 MET cc_start: 0.7654 (mmm) cc_final: 0.7249 (mmm) REVERT: B 28 MET cc_start: 0.3145 (tpt) cc_final: 0.1657 (mpp) REVERT: C 364 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7407 (t80) REVERT: C 397 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7065 (mpp80) REVERT: C 484 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6517 (tp30) REVERT: E 75 GLN cc_start: 0.8726 (tm-30) cc_final: 0.7845 (tm-30) REVERT: E 101 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7947 (tm-30) REVERT: F 129 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7380 (t70) REVERT: F 516 MET cc_start: 0.7733 (mmm) cc_final: 0.7343 (mmm) REVERT: F 536 MET cc_start: 0.8440 (mmt) cc_final: 0.8219 (mmt) REVERT: F 562 MET cc_start: 0.8673 (ppp) cc_final: 0.8323 (ppp) REVERT: F 646 TYR cc_start: 0.7604 (t80) cc_final: 0.7343 (t80) REVERT: H 463 MET cc_start: 0.9110 (tpp) cc_final: 0.8888 (tpp) REVERT: H 469 MET cc_start: 0.8861 (ttm) cc_final: 0.8493 (ttp) REVERT: H 516 MET cc_start: 0.7679 (mmm) cc_final: 0.7398 (mmt) REVERT: H 588 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8687 (mtmm) REVERT: I 283 MET cc_start: 0.4689 (tpp) cc_final: 0.4172 (tpp) REVERT: I 363 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8715 (mm) REVERT: I 529 MET cc_start: 0.8525 (mtp) cc_final: 0.8063 (mmm) REVERT: J 170 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8123 (pt) REVERT: J 283 GLU cc_start: 0.8003 (tp30) cc_final: 0.7765 (tm-30) REVERT: J 358 PHE cc_start: 0.8022 (m-80) cc_final: 0.7741 (m-10) REVERT: K 378 TYR cc_start: 0.7243 (m-80) cc_final: 0.7038 (m-80) REVERT: M 28 ASP cc_start: 0.7600 (m-30) cc_final: 0.7232 (m-30) REVERT: N 277 CYS cc_start: 0.7034 (p) cc_final: 0.6677 (p) REVERT: N 290 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.5678 (m170) REVERT: N 418 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8066 (tm-30) REVERT: N 564 MET cc_start: 0.4874 (mmt) cc_final: 0.4046 (tmm) REVERT: N 772 ARG cc_start: 0.7402 (mpt90) cc_final: 0.6589 (mmm160) REVERT: O 113 ASP cc_start: 0.8252 (m-30) cc_final: 0.7770 (p0) REVERT: O 239 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7572 (tp30) REVERT: O 444 MET cc_start: 0.8891 (mmm) cc_final: 0.8500 (tpp) REVERT: O 646 MET cc_start: 0.7275 (mmp) cc_final: 0.7064 (ttt) REVERT: O 682 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8157 (pttt) REVERT: O 735 MET cc_start: 0.8271 (ppp) cc_final: 0.7701 (mmp) REVERT: O 751 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7395 (pp) REVERT: P 54 TRP cc_start: 0.7922 (t60) cc_final: 0.7708 (t60) REVERT: P 84 MET cc_start: 0.7537 (mmm) cc_final: 0.7178 (tpp) REVERT: P 286 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7530 (t80) REVERT: P 371 MET cc_start: 0.7663 (tpp) cc_final: 0.7356 (tpp) REVERT: P 435 MET cc_start: 0.8047 (mmm) cc_final: 0.7769 (mtt) REVERT: P 444 GLU cc_start: 0.8504 (tt0) cc_final: 0.7869 (tm-30) REVERT: Q 222 MET cc_start: 0.3901 (mmm) cc_final: 0.3668 (mmt) REVERT: Q 451 MET cc_start: 0.8472 (ttp) cc_final: 0.8102 (ttm) REVERT: R 118 LEU cc_start: 0.7871 (mt) cc_final: 0.7516 (pp) REVERT: R 176 LEU cc_start: 0.8233 (mp) cc_final: 0.7960 (mt) REVERT: R 217 LEU cc_start: 0.8230 (tp) cc_final: 0.7988 (mm) REVERT: R 240 TYR cc_start: 0.7682 (m-10) cc_final: 0.7446 (m-10) REVERT: S 134 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7594 (mm-30) REVERT: S 138 MET cc_start: 0.8337 (tpp) cc_final: 0.8093 (tpp) REVERT: S 139 TYR cc_start: 0.8497 (m-80) cc_final: 0.7680 (m-80) REVERT: X 174 MET cc_start: 0.8601 (mtp) cc_final: 0.8369 (mtp) REVERT: X 304 LEU cc_start: 0.7723 (tp) cc_final: 0.7381 (tp) REVERT: X 529 MET cc_start: 0.3215 (mmt) cc_final: 0.3007 (mmm) REVERT: Y 63 MET cc_start: 0.8729 (ptp) cc_final: 0.8486 (mtm) REVERT: Y 142 MET cc_start: 0.8483 (mmm) cc_final: 0.8203 (mmm) REVERT: Y 173 MET cc_start: 0.8493 (tpt) cc_final: 0.7637 (tpt) REVERT: Y 294 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6792 (t80) REVERT: Y 498 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5556 (tp) outliers start: 204 outliers final: 139 residues processed: 783 average time/residue: 0.6758 time to fit residues: 929.3180 Evaluate side-chains 699 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 547 time to evaluate : 6.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1373 MET Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 414 PHE Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 643 PHE Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 209 LEU Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 177 PHE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 238 GLU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 290 HIS Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 557 CYS Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 629 LEU Chi-restraints excluded: chain N residue 646 MET Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 112 PHE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 508 MET Chi-restraints excluded: chain O residue 514 ILE Chi-restraints excluded: chain O residue 599 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 612 LYS Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 682 LYS Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 409 TYR Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 259 LYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 333 VAL Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 221 VAL Chi-restraints excluded: chain X residue 44 MET Chi-restraints excluded: chain X residue 63 MET Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 239 TRP Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 413 LEU Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 195 VAL Chi-restraints excluded: chain Y residue 209 LEU Chi-restraints excluded: chain Y residue 294 PHE Chi-restraints excluded: chain Y residue 331 LEU Chi-restraints excluded: chain Y residue 347 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 498 LEU Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 542 optimal weight: 2.9990 chunk 350 optimal weight: 20.0000 chunk 523 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 557 optimal weight: 50.0000 chunk 597 optimal weight: 4.9990 chunk 433 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 689 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 601 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 502 GLN I 737 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 HIS K 264 HIS ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 HIS R 224 GLN ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 GLN ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 505 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 73849 Z= 0.294 Angle : 0.719 16.291 100078 Z= 0.366 Chirality : 0.043 0.341 11236 Planarity : 0.004 0.072 12735 Dihedral : 5.457 69.069 9978 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 2.71 % Allowed : 20.67 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.87 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.09), residues: 9052 helix: 1.02 (0.07), residues: 5686 sheet: -0.95 (0.18), residues: 744 loop : -2.22 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1386 HIS 0.014 0.001 HIS J 314 PHE 0.045 0.002 PHE K 167 TYR 0.060 0.002 TYR J 212 ARG 0.023 0.001 ARG F 520 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 530 time to evaluate : 6.381 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 210 MET cc_start: 0.8258 (mmt) cc_final: 0.7986 (mmt) REVERT: A 257 MET cc_start: 0.8568 (tpt) cc_final: 0.8039 (mmm) REVERT: A 1070 LEU cc_start: 0.9495 (tp) cc_final: 0.9210 (tp) REVERT: A 1191 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8495 (pt) REVERT: A 1786 MET cc_start: 0.7706 (mmm) cc_final: 0.7316 (mmm) REVERT: B 28 MET cc_start: 0.3244 (tpt) cc_final: 0.1742 (mpp) REVERT: C 397 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7176 (mpp80) REVERT: F 536 MET cc_start: 0.8550 (mmt) cc_final: 0.8311 (mmt) REVERT: F 562 MET cc_start: 0.8613 (ppp) cc_final: 0.8359 (ppp) REVERT: H 463 MET cc_start: 0.9177 (tpp) cc_final: 0.8964 (tpp) REVERT: H 469 MET cc_start: 0.8944 (ttm) cc_final: 0.8573 (ttp) REVERT: H 516 MET cc_start: 0.7887 (mmm) cc_final: 0.7611 (mmt) REVERT: H 588 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8583 (mppt) REVERT: I 283 MET cc_start: 0.4791 (tpp) cc_final: 0.4305 (tpp) REVERT: I 330 LEU cc_start: 0.7803 (tt) cc_final: 0.7488 (pp) REVERT: I 363 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8801 (mm) REVERT: I 422 TYR cc_start: 0.7874 (t80) cc_final: 0.7659 (t80) REVERT: I 529 MET cc_start: 0.8584 (mtp) cc_final: 0.8075 (mmm) REVERT: I 548 MET cc_start: 0.5845 (mmm) cc_final: 0.5590 (mmm) REVERT: I 737 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8779 (t0) REVERT: J 170 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8223 (pt) REVERT: J 358 PHE cc_start: 0.8201 (m-80) cc_final: 0.7924 (m-10) REVERT: K 258 MET cc_start: 0.7910 (tpp) cc_final: 0.7480 (tpp) REVERT: N 285 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: N 290 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.5796 (m170) REVERT: N 418 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8142 (tm-30) REVERT: N 564 MET cc_start: 0.5247 (mmt) cc_final: 0.3798 (tmm) REVERT: N 632 MET cc_start: 0.4888 (ttp) cc_final: 0.4564 (ttp) REVERT: O 444 MET cc_start: 0.8949 (mmm) cc_final: 0.8517 (tpp) REVERT: O 460 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6917 (tp40) REVERT: O 646 MET cc_start: 0.7358 (mmp) cc_final: 0.7076 (ttt) REVERT: O 735 MET cc_start: 0.8323 (ppp) cc_final: 0.7713 (mmp) REVERT: O 751 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7705 (pp) REVERT: P 84 MET cc_start: 0.7641 (mmm) cc_final: 0.7271 (tpp) REVERT: P 286 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7728 (t80) REVERT: P 371 MET cc_start: 0.7753 (tpp) cc_final: 0.7396 (tpp) REVERT: P 435 MET cc_start: 0.8169 (mmm) cc_final: 0.7840 (mtt) REVERT: P 444 GLU cc_start: 0.8574 (tt0) cc_final: 0.7978 (tm-30) REVERT: Q 451 MET cc_start: 0.8511 (ttp) cc_final: 0.8165 (ttm) REVERT: R 118 LEU cc_start: 0.8001 (mt) cc_final: 0.7561 (pp) REVERT: R 176 LEU cc_start: 0.8143 (mp) cc_final: 0.7919 (mt) REVERT: R 217 LEU cc_start: 0.8099 (tp) cc_final: 0.7788 (mm) REVERT: R 240 TYR cc_start: 0.7816 (m-10) cc_final: 0.7526 (m-10) REVERT: S 138 MET cc_start: 0.8437 (tpp) cc_final: 0.8223 (tpp) REVERT: X 400 ILE cc_start: 0.8884 (pt) cc_final: 0.8574 (tp) REVERT: Y 63 MET cc_start: 0.8757 (ptp) cc_final: 0.8525 (mtm) REVERT: Y 142 MET cc_start: 0.8312 (mmm) cc_final: 0.7916 (mmm) REVERT: Y 173 MET cc_start: 0.8555 (tpt) cc_final: 0.7716 (tpt) REVERT: Y 294 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6769 (t80) REVERT: Y 498 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5765 (tp) outliers start: 206 outliers final: 171 residues processed: 700 average time/residue: 0.6388 time to fit residues: 795.3278 Evaluate side-chains 690 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 506 time to evaluate : 8.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1373 MET Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1491 PHE Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1581 ILE Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 712 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 643 PHE Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 737 ASN Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 289 HIS Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain K residue 79 CYS Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 293 ASP Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 397 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 177 PHE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 238 GLU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain N residue 290 HIS Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 557 CYS Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 641 LEU Chi-restraints excluded: chain N residue 646 MET Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 112 PHE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 417 LEU Chi-restraints excluded: chain O residue 460 GLN Chi-restraints excluded: chain O residue 508 MET Chi-restraints excluded: chain O residue 514 ILE Chi-restraints excluded: chain O residue 599 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 409 TYR Chi-restraints excluded: chain Q residue 188 ASN Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 259 LYS Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 224 GLN Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 333 VAL Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 221 VAL Chi-restraints excluded: chain X residue 44 MET Chi-restraints excluded: chain X residue 63 MET Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 239 TRP Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain X residue 413 LEU Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 195 VAL Chi-restraints excluded: chain Y residue 199 CYS Chi-restraints excluded: chain Y residue 209 LEU Chi-restraints excluded: chain Y residue 271 VAL Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 294 PHE Chi-restraints excluded: chain Y residue 331 LEU Chi-restraints excluded: chain Y residue 334 ILE Chi-restraints excluded: chain Y residue 347 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 498 LEU Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 797 optimal weight: 0.0170 chunk 840 optimal weight: 20.0000 chunk 766 optimal weight: 30.0000 chunk 817 optimal weight: 8.9990 chunk 491 optimal weight: 9.9990 chunk 356 optimal weight: 0.5980 chunk 641 optimal weight: 4.9990 chunk 250 optimal weight: 0.9990 chunk 738 optimal weight: 7.9990 chunk 773 optimal weight: 2.9990 chunk 814 optimal weight: 0.8980 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 737 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 264 HIS ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 571 ASN ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 370 HIS ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 HIS ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 505 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 73849 Z= 0.188 Angle : 0.687 16.376 100078 Z= 0.346 Chirality : 0.042 0.341 11236 Planarity : 0.004 0.071 12735 Dihedral : 5.371 69.139 9978 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.41 % Favored : 93.56 % Rotamer: Outliers : 2.48 % Allowed : 21.20 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.58 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.09), residues: 9052 helix: 1.09 (0.07), residues: 5702 sheet: -0.89 (0.18), residues: 749 loop : -2.18 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 418 HIS 0.011 0.001 HIS J 314 PHE 0.032 0.002 PHE J 164 TYR 0.054 0.001 TYR J 212 ARG 0.012 0.000 ARG F 520 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 579 time to evaluate : 6.438 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 74 TRP cc_start: 0.8818 (p90) cc_final: 0.8562 (p90) REVERT: A 257 MET cc_start: 0.8494 (tpt) cc_final: 0.8144 (mmm) REVERT: A 1070 LEU cc_start: 0.9463 (tp) cc_final: 0.9173 (tp) REVERT: A 1786 MET cc_start: 0.7742 (mmm) cc_final: 0.7404 (mmm) REVERT: B 28 MET cc_start: 0.3134 (tpt) cc_final: 0.1650 (mpp) REVERT: B 77 ARG cc_start: 0.3748 (OUTLIER) cc_final: 0.1456 (mmt180) REVERT: C 397 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7079 (mpp80) REVERT: E 101 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7958 (tm-30) REVERT: F 516 MET cc_start: 0.7345 (mmm) cc_final: 0.7097 (tpp) REVERT: F 562 MET cc_start: 0.8485 (ppp) cc_final: 0.8252 (ppp) REVERT: F 646 TYR cc_start: 0.7621 (t80) cc_final: 0.7407 (t80) REVERT: H 463 MET cc_start: 0.9124 (tpp) cc_final: 0.8769 (tpp) REVERT: H 469 MET cc_start: 0.8883 (ttm) cc_final: 0.8531 (ttp) REVERT: H 516 MET cc_start: 0.7700 (mmm) cc_final: 0.7419 (mmt) REVERT: H 588 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8667 (mtmm) REVERT: I 283 MET cc_start: 0.5163 (tpp) cc_final: 0.4743 (tpp) REVERT: I 330 LEU cc_start: 0.7819 (tt) cc_final: 0.7563 (pp) REVERT: I 363 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8731 (mm) REVERT: I 403 LEU cc_start: 0.7803 (tt) cc_final: 0.7449 (mm) REVERT: I 422 TYR cc_start: 0.7840 (t80) cc_final: 0.7523 (t80) REVERT: I 440 MET cc_start: 0.7868 (mmp) cc_final: 0.7220 (tmm) REVERT: I 548 MET cc_start: 0.6301 (mmm) cc_final: 0.5915 (mmm) REVERT: I 737 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8727 (t0) REVERT: J 170 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8154 (pt) REVERT: J 283 GLU cc_start: 0.8007 (tp30) cc_final: 0.7770 (tm-30) REVERT: J 358 PHE cc_start: 0.8009 (m-80) cc_final: 0.7751 (m-10) REVERT: L 153 MET cc_start: 0.8240 (tpp) cc_final: 0.7966 (tpt) REVERT: N 277 CYS cc_start: 0.7212 (p) cc_final: 0.6780 (p) REVERT: N 285 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: N 290 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.5672 (m170) REVERT: N 414 MET cc_start: 0.5804 (ptt) cc_final: 0.5409 (ptt) REVERT: N 418 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8088 (tm-30) REVERT: N 564 MET cc_start: 0.4793 (mmt) cc_final: 0.3869 (tmm) REVERT: N 632 MET cc_start: 0.4756 (ttp) cc_final: 0.4391 (ttp) REVERT: O 239 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7873 (mp0) REVERT: O 444 MET cc_start: 0.8893 (mmm) cc_final: 0.8574 (tpp) REVERT: O 460 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6804 (tp40) REVERT: O 646 MET cc_start: 0.7374 (mmp) cc_final: 0.7051 (ttt) REVERT: O 735 MET cc_start: 0.8285 (ppp) cc_final: 0.7730 (mmp) REVERT: O 751 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7663 (pp) REVERT: P 54 TRP cc_start: 0.7948 (t60) cc_final: 0.7722 (t60) REVERT: P 84 MET cc_start: 0.7527 (mmm) cc_final: 0.7151 (tpp) REVERT: P 286 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7617 (t80) REVERT: P 371 MET cc_start: 0.7683 (tpp) cc_final: 0.7371 (tpp) REVERT: P 435 MET cc_start: 0.8047 (mmm) cc_final: 0.7811 (mtt) REVERT: P 444 GLU cc_start: 0.8536 (tt0) cc_final: 0.7947 (tm-30) REVERT: Q 451 MET cc_start: 0.8510 (ttp) cc_final: 0.8239 (ttm) REVERT: R 118 LEU cc_start: 0.7880 (mt) cc_final: 0.7531 (pp) REVERT: R 176 LEU cc_start: 0.8236 (mp) cc_final: 0.7971 (mt) REVERT: R 217 LEU cc_start: 0.8170 (tp) cc_final: 0.7888 (mm) REVERT: R 240 TYR cc_start: 0.7781 (m-10) cc_final: 0.7476 (m-10) REVERT: S 138 MET cc_start: 0.8333 (tpp) cc_final: 0.7498 (tmm) REVERT: S 304 LYS cc_start: 0.7395 (ptpp) cc_final: 0.6980 (tmmt) REVERT: X 400 ILE cc_start: 0.8837 (pt) cc_final: 0.8426 (tp) REVERT: Y 63 MET cc_start: 0.8668 (ptp) cc_final: 0.8444 (mtm) REVERT: Y 142 MET cc_start: 0.8308 (mmm) cc_final: 0.7972 (mmm) REVERT: Y 173 MET cc_start: 0.8419 (tpt) cc_final: 0.7589 (tpt) REVERT: Y 294 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6895 (t80) REVERT: Y 498 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5715 (tp) REVERT: Z 112 ASP cc_start: 0.7439 (m-30) cc_final: 0.6659 (t70) outliers start: 188 outliers final: 148 residues processed: 726 average time/residue: 0.7173 time to fit residues: 933.0062 Evaluate side-chains 698 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 537 time to evaluate : 6.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1373 MET Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 712 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 414 PHE Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 643 PHE Chi-restraints excluded: chain I residue 717 MET Chi-restraints excluded: chain I residue 737 ASN Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 289 HIS Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 441 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 293 ASP Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 238 GLU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain N residue 290 HIS Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 557 CYS Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 646 MET Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 112 PHE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 417 LEU Chi-restraints excluded: chain O residue 460 GLN Chi-restraints excluded: chain O residue 506 LEU Chi-restraints excluded: chain O residue 508 MET Chi-restraints excluded: chain O residue 514 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 409 TYR Chi-restraints excluded: chain Q residue 188 ASN Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 259 LYS Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 333 VAL Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 221 VAL Chi-restraints excluded: chain X residue 44 MET Chi-restraints excluded: chain X residue 63 MET Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 239 TRP Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 195 VAL Chi-restraints excluded: chain Y residue 209 LEU Chi-restraints excluded: chain Y residue 271 VAL Chi-restraints excluded: chain Y residue 294 PHE Chi-restraints excluded: chain Y residue 331 LEU Chi-restraints excluded: chain Y residue 347 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 498 LEU Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 536 optimal weight: 1.9990 chunk 864 optimal weight: 0.9980 chunk 527 optimal weight: 2.9990 chunk 410 optimal weight: 0.7980 chunk 600 optimal weight: 4.9990 chunk 906 optimal weight: 0.0170 chunk 834 optimal weight: 5.9990 chunk 721 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 557 optimal weight: 9.9990 chunk 442 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 674 HIS ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 609 HIS ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 HIS J 414 GLN ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN M 6 GLN ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 370 HIS ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 HIS ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 ASN ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 298 GLN ** Y 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 505 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 73849 Z= 0.181 Angle : 0.690 16.348 100078 Z= 0.345 Chirality : 0.041 0.340 11236 Planarity : 0.004 0.069 12735 Dihedral : 5.257 69.045 9976 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.61 % Favored : 93.36 % Rotamer: Outliers : 2.21 % Allowed : 21.71 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.58 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.09), residues: 9052 helix: 1.15 (0.07), residues: 5703 sheet: -0.82 (0.18), residues: 761 loop : -2.16 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 14 HIS 0.011 0.001 HIS X 89 PHE 0.041 0.002 PHE N 531 TYR 0.060 0.001 TYR J 212 ARG 0.033 0.000 ARG I 739 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18104 Ramachandran restraints generated. 9052 Oldfield, 0 Emsley, 9052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 592 time to evaluate : 6.379 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 74 TRP cc_start: 0.8812 (p90) cc_final: 0.8559 (p90) REVERT: A 257 MET cc_start: 0.8482 (tpt) cc_final: 0.8144 (mmm) REVERT: A 1070 LEU cc_start: 0.9453 (tp) cc_final: 0.9166 (tp) REVERT: A 1296 LEU cc_start: 0.8277 (tt) cc_final: 0.8043 (tt) REVERT: A 1551 ASN cc_start: 0.7398 (p0) cc_final: 0.7188 (p0) REVERT: B 28 MET cc_start: 0.3038 (tpt) cc_final: 0.1596 (mpp) REVERT: B 77 ARG cc_start: 0.3756 (OUTLIER) cc_final: 0.1482 (mmt180) REVERT: C 397 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7028 (mpp80) REVERT: C 414 MET cc_start: 0.7851 (mtp) cc_final: 0.7594 (mtm) REVERT: E 101 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7833 (tm-30) REVERT: F 516 MET cc_start: 0.7228 (mmm) cc_final: 0.6986 (tpp) REVERT: F 562 MET cc_start: 0.8515 (ppp) cc_final: 0.8299 (ppp) REVERT: F 646 TYR cc_start: 0.7510 (t80) cc_final: 0.7276 (t80) REVERT: H 463 MET cc_start: 0.9095 (tpp) cc_final: 0.8712 (tpp) REVERT: H 469 MET cc_start: 0.8879 (ttm) cc_final: 0.8522 (ttp) REVERT: H 516 MET cc_start: 0.7738 (mmm) cc_final: 0.7515 (mmt) REVERT: H 588 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8658 (mtmm) REVERT: I 283 MET cc_start: 0.5207 (tpp) cc_final: 0.4819 (tpp) REVERT: I 363 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8691 (mm) REVERT: I 403 LEU cc_start: 0.7772 (tt) cc_final: 0.7421 (mm) REVERT: I 422 TYR cc_start: 0.7770 (t80) cc_final: 0.7423 (t80) REVERT: I 440 MET cc_start: 0.7873 (mmp) cc_final: 0.7163 (tmm) REVERT: I 548 MET cc_start: 0.6469 (mmm) cc_final: 0.6102 (mmm) REVERT: J 170 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8174 (pt) REVERT: J 283 GLU cc_start: 0.7939 (tp30) cc_final: 0.7726 (tm-30) REVERT: J 358 PHE cc_start: 0.7992 (m-80) cc_final: 0.7735 (m-10) REVERT: M 28 ASP cc_start: 0.7599 (m-30) cc_final: 0.7224 (m-30) REVERT: N 277 CYS cc_start: 0.7199 (p) cc_final: 0.6746 (p) REVERT: N 285 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7418 (m-10) REVERT: N 414 MET cc_start: 0.5676 (ptt) cc_final: 0.5212 (ptt) REVERT: N 564 MET cc_start: 0.4847 (mmt) cc_final: 0.3849 (tmm) REVERT: N 632 MET cc_start: 0.4570 (ttp) cc_final: 0.4336 (ttp) REVERT: N 776 MET cc_start: 0.5637 (ptp) cc_final: 0.5163 (pmm) REVERT: O 444 MET cc_start: 0.8949 (mmm) cc_final: 0.8569 (tpp) REVERT: O 460 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6717 (tp40) REVERT: O 603 MET cc_start: 0.7949 (mmm) cc_final: 0.7730 (mmt) REVERT: O 646 MET cc_start: 0.7372 (mmp) cc_final: 0.7059 (ttt) REVERT: O 735 MET cc_start: 0.8091 (ppp) cc_final: 0.7696 (mmp) REVERT: P 54 TRP cc_start: 0.7843 (t60) cc_final: 0.7509 (t60) REVERT: P 84 MET cc_start: 0.7553 (mmm) cc_final: 0.7153 (tpp) REVERT: P 286 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7650 (t80) REVERT: P 371 MET cc_start: 0.7688 (tpp) cc_final: 0.7372 (tpp) REVERT: P 435 MET cc_start: 0.8032 (mmm) cc_final: 0.7761 (mtt) REVERT: P 444 GLU cc_start: 0.8571 (tt0) cc_final: 0.7902 (tm-30) REVERT: P 498 TYR cc_start: 0.6881 (t80) cc_final: 0.6315 (t80) REVERT: Q 451 MET cc_start: 0.8541 (ttp) cc_final: 0.8270 (ttm) REVERT: R 118 LEU cc_start: 0.7939 (mt) cc_final: 0.7588 (pp) REVERT: R 176 LEU cc_start: 0.8289 (mp) cc_final: 0.8026 (mt) REVERT: R 217 LEU cc_start: 0.8247 (tp) cc_final: 0.7962 (mm) REVERT: R 240 TYR cc_start: 0.7631 (m-10) cc_final: 0.7359 (m-10) REVERT: R 316 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8405 (ttm110) REVERT: S 134 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7636 (mm-30) REVERT: S 138 MET cc_start: 0.8342 (tpp) cc_final: 0.7569 (tmm) REVERT: S 304 LYS cc_start: 0.7312 (ptpp) cc_final: 0.6900 (tmmt) REVERT: Y 142 MET cc_start: 0.8391 (mmm) cc_final: 0.8176 (mmm) REVERT: Y 173 MET cc_start: 0.8386 (tpt) cc_final: 0.7552 (tpt) REVERT: Y 294 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7042 (t80) REVERT: Y 498 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5583 (tp) REVERT: Z 112 ASP cc_start: 0.7435 (m-30) cc_final: 0.6667 (t70) outliers start: 168 outliers final: 134 residues processed: 722 average time/residue: 0.6443 time to fit residues: 822.3972 Evaluate side-chains 689 residues out of total 8042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 545 time to evaluate : 6.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1373 MET Chi-restraints excluded: chain A residue 1487 CYS Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1581 ILE Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 CYS Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 576 CYS Chi-restraints excluded: chain H residue 588 LYS Chi-restraints excluded: chain H residue 618 ASP Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 712 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 414 PHE Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 643 PHE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 441 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 293 ASP Chi-restraints excluded: chain K residue 307 CYS Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 238 GLU Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 285 PHE Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 541 ASN Chi-restraints excluded: chain N residue 557 CYS Chi-restraints excluded: chain N residue 595 ILE Chi-restraints excluded: chain N residue 646 MET Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 112 PHE Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 417 LEU Chi-restraints excluded: chain O residue 460 GLN Chi-restraints excluded: chain O residue 508 MET Chi-restraints excluded: chain O residue 514 ILE Chi-restraints excluded: chain O residue 599 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 685 GLU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 409 TYR Chi-restraints excluded: chain Q residue 188 ASN Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 259 LYS Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 333 VAL Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain S residue 221 VAL Chi-restraints excluded: chain X residue 44 MET Chi-restraints excluded: chain X residue 63 MET Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 239 TRP Chi-restraints excluded: chain X residue 271 VAL Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 195 VAL Chi-restraints excluded: chain Y residue 294 PHE Chi-restraints excluded: chain Y residue 347 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 496 ILE Chi-restraints excluded: chain Y residue 498 LEU Chi-restraints excluded: chain Y residue 509 CYS Chi-restraints excluded: chain Y residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 573 optimal weight: 9.9990 chunk 769 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 665 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 723 optimal weight: 20.0000 chunk 302 optimal weight: 5.9990 chunk 742 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS C 107 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 414 GLN K 213 ASN ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 ASN O 370 HIS ** O 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 754 HIS ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 HIS ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.082816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067468 restraints weight = 331494.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068653 restraints weight = 201117.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.069252 restraints weight = 123742.703| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 73849 Z= 0.366 Angle : 0.798 16.524 100078 Z= 0.404 Chirality : 0.045 0.341 11236 Planarity : 0.005 0.161 12735 Dihedral : 5.514 68.779 9976 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.47 % Favored : 92.50 % Rotamer: Outliers : 2.34 % Allowed : 21.87 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.32 % Twisted Proline : 0.87 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.09), residues: 9052 helix: 0.92 (0.07), residues: 5681 sheet: -0.96 (0.18), residues: 764 loop : -2.21 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 418 HIS 0.011 0.001 HIS X 89 PHE 0.046 0.002 PHE J 164 TYR 0.061 0.002 TYR J 212 ARG 0.013 0.001 ARG J 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15005.19 seconds wall clock time: 263 minutes 36.01 seconds (15816.01 seconds total)