Starting phenix.real_space_refine on Sat Feb 24 14:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sic_25140/02_2024/7sic_25140_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sic_25140/02_2024/7sic_25140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sic_25140/02_2024/7sic_25140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sic_25140/02_2024/7sic_25140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sic_25140/02_2024/7sic_25140_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sic_25140/02_2024/7sic_25140_updated.pdb" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 306 5.16 5 C 28420 2.51 5 N 7560 2.21 5 O 8190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 58": "OD1" <-> "OD2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 658": "OD1" <-> "OD2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 739": "OE1" <-> "OE2" Residue "A PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1215": "OD1" <-> "OD2" Residue "A ASP 1266": "OD1" <-> "OD2" Residue "A PHE 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1428": "OE1" <-> "OE2" Residue "A ASP 1452": "OD1" <-> "OD2" Residue "A ASP 1467": "OD1" <-> "OD2" Residue "A ASP 1511": "OD1" <-> "OD2" Residue "A ASP 1540": "OD1" <-> "OD2" Residue "A ASP 1573": "OD1" <-> "OD2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A ASP 1641": "OD1" <-> "OD2" Residue "A GLU 1704": "OE1" <-> "OE2" Residue "A ASP 1705": "OD1" <-> "OD2" Residue "A GLU 1991": "OE1" <-> "OE2" Residue "A GLU 1996": "OE1" <-> "OE2" Residue "A ASP 2003": "OD1" <-> "OD2" Residue "A GLU 2007": "OE1" <-> "OE2" Residue "A GLU 2039": "OE1" <-> "OE2" Residue "A GLU 2139": "OE1" <-> "OE2" Residue "A GLU 2157": "OE1" <-> "OE2" Residue "A GLU 2187": "OE1" <-> "OE2" Residue "A PHE 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2200": "OE1" <-> "OE2" Residue "A ASP 2216": "OD1" <-> "OD2" Residue "A GLU 2232": "OE1" <-> "OE2" Residue "A GLU 2347": "OE1" <-> "OE2" Residue "A ASP 2395": "OD1" <-> "OD2" Residue "A TYR 2398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2409": "OE1" <-> "OE2" Residue "A TYR 2437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2448": "OD1" <-> "OD2" Residue "A GLU 2479": "OE1" <-> "OE2" Residue "A TYR 2514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2595": "OD1" <-> "OD2" Residue "A ASP 2597": "OD1" <-> "OD2" Residue "A GLU 2600": "OE1" <-> "OE2" Residue "A GLU 2711": "OE1" <-> "OE2" Residue "A GLU 2744": "OE1" <-> "OE2" Residue "A GLU 2784": "OE1" <-> "OE2" Residue "A PHE 2799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2841": "OD1" <-> "OD2" Residue "A TYR 2969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3015": "OE1" <-> "OE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 658": "OD1" <-> "OD2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "B GLU 739": "OE1" <-> "OE2" Residue "B PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 937": "OE1" <-> "OE2" Residue "B GLU 958": "OE1" <-> "OE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1215": "OD1" <-> "OD2" Residue "B ASP 1266": "OD1" <-> "OD2" Residue "B PHE 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1428": "OE1" <-> "OE2" Residue "B ASP 1452": "OD1" <-> "OD2" Residue "B ASP 1467": "OD1" <-> "OD2" Residue "B ASP 1511": "OD1" <-> "OD2" Residue "B ASP 1540": "OD1" <-> "OD2" Residue "B ASP 1573": "OD1" <-> "OD2" Residue "B GLU 1622": "OE1" <-> "OE2" Residue "B ASP 1641": "OD1" <-> "OD2" Residue "B GLU 1704": "OE1" <-> "OE2" Residue "B ASP 1705": "OD1" <-> "OD2" Residue "B GLU 1991": "OE1" <-> "OE2" Residue "B GLU 1996": "OE1" <-> "OE2" Residue "B ASP 2003": "OD1" <-> "OD2" Residue "B GLU 2007": "OE1" <-> "OE2" Residue "B GLU 2039": "OE1" <-> "OE2" Residue "B GLU 2139": "OE1" <-> "OE2" Residue "B GLU 2157": "OE1" <-> "OE2" Residue "B GLU 2187": "OE1" <-> "OE2" Residue "B PHE 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2200": "OE1" <-> "OE2" Residue "B ASP 2216": "OD1" <-> "OD2" Residue "B GLU 2232": "OE1" <-> "OE2" Residue "B GLU 2347": "OE1" <-> "OE2" Residue "B ASP 2395": "OD1" <-> "OD2" Residue "B TYR 2398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2409": "OE1" <-> "OE2" Residue "B TYR 2437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2448": "OD1" <-> "OD2" Residue "B GLU 2479": "OE1" <-> "OE2" Residue "B TYR 2514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2595": "OD1" <-> "OD2" Residue "B ASP 2597": "OD1" <-> "OD2" Residue "B GLU 2600": "OE1" <-> "OE2" Residue "B GLU 2711": "OE1" <-> "OE2" Residue "B GLU 2744": "OE1" <-> "OE2" Residue "B GLU 2784": "OE1" <-> "OE2" Residue "B PHE 2799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2841": "OD1" <-> "OD2" Residue "B TYR 2969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3015": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44484 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 22210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2773, 22210 Classifications: {'peptide': 2773} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2684} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 22210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2773, 22210 Classifications: {'peptide': 2773} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2684} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.29, per 1000 atoms: 0.46 Number of scatterers: 44484 At special positions: 0 Unit cell: (224.928, 112.992, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 306 16.00 P 6 15.00 Mg 2 11.99 O 8190 8.00 N 7560 7.00 C 28420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.80 Conformation dependent library (CDL) restraints added in 7.5 seconds 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 296 helices and 6 sheets defined 68.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 20.68 Creating SS restraints... Processing helix chain 'A' and resid 6 through 16 Processing helix chain 'A' and resid 20 through 33 removed outlier: 3.959A pdb=" N LYS A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.808A pdb=" N GLU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 108 removed outlier: 3.837A pdb=" N LYS A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.545A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.545A pdb=" N SER A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 3.845A pdb=" N ASP A 211 " --> pdb=" O LYS A 208 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 213 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N CYS A 219 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 removed outlier: 3.582A pdb=" N ALA A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 268 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 407 through 422 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 432 through 443 Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.804A pdb=" N LYS A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 492 removed outlier: 3.642A pdb=" N LYS A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.541A pdb=" N LYS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 525' Processing helix chain 'A' and resid 536 through 548 removed outlier: 3.569A pdb=" N LEU A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 597 through 600 No H-bonds generated for 'chain 'A' and resid 597 through 600' Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.737A pdb=" N THR A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 646 through 655 Processing helix chain 'A' and resid 684 through 704 Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.523A pdb=" N LYS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 765 removed outlier: 3.553A pdb=" N GLU A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 759 " --> pdb=" O CYS A 755 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 786 removed outlier: 4.271A pdb=" N SER A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 778 " --> pdb=" O GLY A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 806 Processing helix chain 'A' and resid 809 through 824 removed outlier: 3.860A pdb=" N SER A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.493A pdb=" N GLN A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N THR A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 removed outlier: 3.922A pdb=" N ILE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 953 Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 984 through 1002 removed outlier: 3.554A pdb=" N LEU A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N HIS A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL A 997 " --> pdb=" O HIS A 993 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 998 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN A1000 " --> pdb=" O HIS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1030 removed outlier: 3.586A pdb=" N VAL A1021 " --> pdb=" O GLN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1052 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 3.611A pdb=" N THR A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU A1078 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 4.987A pdb=" N ASN A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG A1095 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU A1096 " --> pdb=" O SER A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1132 Processing helix chain 'A' and resid 1144 through 1164 Processing helix chain 'A' and resid 1169 through 1181 removed outlier: 3.961A pdb=" N LYS A1181 " --> pdb=" O CYS A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1201 Processing helix chain 'A' and resid 1206 through 1224 removed outlier: 3.874A pdb=" N HIS A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASP A1215 " --> pdb=" O ALA A1211 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR A1216 " --> pdb=" O SER A1212 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1261 removed outlier: 6.015A pdb=" N LYS A1253 " --> pdb=" O ARG A1249 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A1254 " --> pdb=" O SER A1250 " (cutoff:3.500A) Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1265 through 1275 Processing helix chain 'A' and resid 1279 through 1285 Processing helix chain 'A' and resid 1287 through 1297 removed outlier: 3.604A pdb=" N ASN A1293 " --> pdb=" O LYS A1289 " (cutoff:3.500A) Proline residue: A1296 - end of helix Processing helix chain 'A' and resid 1306 through 1322 removed outlier: 4.273A pdb=" N GLN A1310 " --> pdb=" O SER A1306 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN A1311 " --> pdb=" O GLY A1307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1330 No H-bonds generated for 'chain 'A' and resid 1328 through 1330' Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1340 through 1350 removed outlier: 3.650A pdb=" N THR A1350 " --> pdb=" O GLU A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1396 Processing helix chain 'A' and resid 1404 through 1410 Processing helix chain 'A' and resid 1412 through 1428 removed outlier: 3.526A pdb=" N TYR A1415 " --> pdb=" O PRO A1412 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A1418 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A1419 " --> pdb=" O GLN A1416 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A1422 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A1424 " --> pdb=" O ALA A1421 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN A1425 " --> pdb=" O ILE A1422 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A1428 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1452 removed outlier: 3.751A pdb=" N ASP A1452 " --> pdb=" O LEU A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1477 Processing helix chain 'A' and resid 1485 through 1508 Processing helix chain 'A' and resid 1512 through 1514 No H-bonds generated for 'chain 'A' and resid 1512 through 1514' Processing helix chain 'A' and resid 1517 through 1528 Proline residue: A1526 - end of helix Processing helix chain 'A' and resid 1532 through 1546 removed outlier: 3.562A pdb=" N GLN A1537 " --> pdb=" O GLU A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1560 removed outlier: 4.055A pdb=" N ILE A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1582 Processing helix chain 'A' and resid 1590 through 1602 removed outlier: 3.571A pdb=" N SER A1601 " --> pdb=" O PHE A1597 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A1602 " --> pdb=" O LEU A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1623 removed outlier: 4.481A pdb=" N GLU A1612 " --> pdb=" O THR A1609 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1621 " --> pdb=" O ARG A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1634 removed outlier: 3.714A pdb=" N VAL A1629 " --> pdb=" O LYS A1625 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A1630 " --> pdb=" O ASP A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1641 No H-bonds generated for 'chain 'A' and resid 1639 through 1641' Processing helix chain 'A' and resid 1643 through 1658 Processing helix chain 'A' and resid 1664 through 1677 Processing helix chain 'A' and resid 1694 through 1702 removed outlier: 3.525A pdb=" N LEU A1702 " --> pdb=" O LYS A1698 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1723 removed outlier: 4.470A pdb=" N VAL A1723 " --> pdb=" O ASN A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1742 Processing helix chain 'A' and resid 1744 through 1753 Processing helix chain 'A' and resid 1759 through 1763 Processing helix chain 'A' and resid 1792 through 1795 No H-bonds generated for 'chain 'A' and resid 1792 through 1795' Processing helix chain 'A' and resid 1802 through 1815 Processing helix chain 'A' and resid 1822 through 1833 removed outlier: 3.716A pdb=" N LEU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A1827 " --> pdb=" O ILE A1823 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS A1828 " --> pdb=" O LEU A1824 " (cutoff:3.500A) Proline residue: A1829 - end of helix removed outlier: 3.705A pdb=" N VAL A1833 " --> pdb=" O PRO A1829 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1851 Proline residue: A1843 - end of helix Processing helix chain 'A' and resid 1857 through 1875 removed outlier: 3.644A pdb=" N LEU A1874 " --> pdb=" O PHE A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1903 through 1918 removed outlier: 3.655A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1932 removed outlier: 3.999A pdb=" N PHE A1932 " --> pdb=" O PHE A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1947 Processing helix chain 'A' and resid 1951 through 1973 Processing helix chain 'A' and resid 1986 through 1996 Processing helix chain 'A' and resid 2001 through 2012 Processing helix chain 'A' and resid 2016 through 2019 Processing helix chain 'A' and resid 2029 through 2038 Processing helix chain 'A' and resid 2042 through 2051 Processing helix chain 'A' and resid 2057 through 2070 Processing helix chain 'A' and resid 2074 through 2087 Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2124 through 2136 Processing helix chain 'A' and resid 2140 through 2159 Processing helix chain 'A' and resid 2166 through 2168 No H-bonds generated for 'chain 'A' and resid 2166 through 2168' Processing helix chain 'A' and resid 2170 through 2190 removed outlier: 3.613A pdb=" N GLU A2187 " --> pdb=" O GLU A2183 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A2188 " --> pdb=" O SER A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2195 through 2211 Processing helix chain 'A' and resid 2217 through 2236 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2244 through 2264 Processing helix chain 'A' and resid 2269 through 2281 removed outlier: 3.624A pdb=" N TYR A2281 " --> pdb=" O GLN A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2290 through 2301 Processing helix chain 'A' and resid 2305 through 2322 Processing helix chain 'A' and resid 2328 through 2348 removed outlier: 4.119A pdb=" N LEU A2332 " --> pdb=" O PRO A2328 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A2333 " --> pdb=" O SER A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2359 Processing helix chain 'A' and resid 2361 through 2370 Processing helix chain 'A' and resid 2377 through 2405 Processing helix chain 'A' and resid 2408 through 2421 removed outlier: 3.595A pdb=" N LEU A2417 " --> pdb=" O LYS A2413 " (cutoff:3.500A) Processing helix chain 'A' and resid 2437 through 2476 removed outlier: 4.124A pdb=" N GLU A2449 " --> pdb=" O LEU A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2481 through 2494 removed outlier: 3.837A pdb=" N LEU A2490 " --> pdb=" O LEU A2487 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A2492 " --> pdb=" O SER A2489 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A2493 " --> pdb=" O LEU A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2506 Processing helix chain 'A' and resid 2508 through 2510 No H-bonds generated for 'chain 'A' and resid 2508 through 2510' Processing helix chain 'A' and resid 2513 through 2526 Proline residue: A2518 - end of helix removed outlier: 5.257A pdb=" N TYR A2521 " --> pdb=" O PRO A2518 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A2523 " --> pdb=" O MET A2520 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A2525 " --> pdb=" O GLN A2522 " (cutoff:3.500A) Processing helix chain 'A' and resid 2537 through 2551 Processing helix chain 'A' and resid 2553 through 2555 No H-bonds generated for 'chain 'A' and resid 2553 through 2555' Processing helix chain 'A' and resid 2557 through 2564 Processing helix chain 'A' and resid 2568 through 2572 Processing helix chain 'A' and resid 2593 through 2612 removed outlier: 3.964A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2632 Processing helix chain 'A' and resid 2637 through 2640 removed outlier: 4.347A pdb=" N THR A2640 " --> pdb=" O GLN A2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2637 through 2640' Processing helix chain 'A' and resid 2652 through 2655 No H-bonds generated for 'chain 'A' and resid 2652 through 2655' Processing helix chain 'A' and resid 2723 through 2740 Processing helix chain 'A' and resid 2743 through 2747 Processing helix chain 'A' and resid 2776 through 2781 Processing helix chain 'A' and resid 2787 through 2791 Processing helix chain 'A' and resid 2798 through 2807 Processing helix chain 'A' and resid 2813 through 2825 Processing helix chain 'A' and resid 2831 through 2838 removed outlier: 3.900A pdb=" N CYS A2835 " --> pdb=" O ARG A2832 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A2836 " --> pdb=" O TYR A2833 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A2837 " --> pdb=" O PHE A2834 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A2838 " --> pdb=" O CYS A2835 " (cutoff:3.500A) Processing helix chain 'A' and resid 2842 through 2866 Processing helix chain 'A' and resid 2873 through 2875 No H-bonds generated for 'chain 'A' and resid 2873 through 2875' Processing helix chain 'A' and resid 2897 through 2899 No H-bonds generated for 'chain 'A' and resid 2897 through 2899' Processing helix chain 'A' and resid 2912 through 2918 removed outlier: 3.772A pdb=" N MET A2918 " --> pdb=" O ILE A2914 " (cutoff:3.500A) Processing helix chain 'A' and resid 2926 through 2940 Processing helix chain 'A' and resid 2942 through 2953 Processing helix chain 'A' and resid 2964 through 2970 Processing helix chain 'A' and resid 3002 through 3018 Processing helix chain 'A' and resid 3028 through 3040 Processing helix chain 'A' and resid 3042 through 3047 removed outlier: 3.731A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3052 No H-bonds generated for 'chain 'A' and resid 3050 through 3052' Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.959A pdb=" N LYS B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 57 through 73 removed outlier: 3.808A pdb=" N GLU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 108 removed outlier: 3.838A pdb=" N LYS B 92 " --> pdb=" O SER B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.545A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 183 through 201 removed outlier: 3.545A pdb=" N SER B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.845A pdb=" N ASP B 211 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 213 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS B 219 " --> pdb=" O ALA B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 3.582A pdb=" N ALA B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 268 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'B' and resid 343 through 356 Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 407 through 422 Proline residue: B 411 - end of helix Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 432 through 443 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.803A pdb=" N LYS B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 492 removed outlier: 3.642A pdb=" N LYS B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 513 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.541A pdb=" N LYS B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 521 through 525' Processing helix chain 'B' and resid 536 through 548 removed outlier: 3.569A pdb=" N LEU B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 597 through 600 No H-bonds generated for 'chain 'B' and resid 597 through 600' Processing helix chain 'B' and resid 608 through 616 removed outlier: 3.737A pdb=" N THR B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 628 Processing helix chain 'B' and resid 646 through 655 Processing helix chain 'B' and resid 684 through 704 Processing helix chain 'B' and resid 713 through 731 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.523A pdb=" N LYS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 765 removed outlier: 3.553A pdb=" N GLU B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 759 " --> pdb=" O CYS B 755 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.271A pdb=" N SER B 775 " --> pdb=" O PHE B 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 778 " --> pdb=" O GLY B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 809 through 824 removed outlier: 3.860A pdb=" N SER B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 889 No H-bonds generated for 'chain 'B' and resid 887 through 889' Processing helix chain 'B' and resid 892 through 913 removed outlier: 4.493A pdb=" N GLN B 912 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 931 removed outlier: 3.922A pdb=" N ILE B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 953 Processing helix chain 'B' and resid 963 through 971 Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 984 through 1002 removed outlier: 3.554A pdb=" N LEU B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N HIS B 996 " --> pdb=" O ASN B 992 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL B 997 " --> pdb=" O HIS B 993 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 998 " --> pdb=" O VAL B 994 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B1000 " --> pdb=" O HIS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1030 removed outlier: 3.586A pdb=" N VAL B1021 " --> pdb=" O GLN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1052 Processing helix chain 'B' and resid 1070 through 1079 removed outlier: 3.611A pdb=" N THR B1075 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B1076 " --> pdb=" O GLU B1072 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE B1077 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU B1078 " --> pdb=" O PHE B1074 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA B1079 " --> pdb=" O THR B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1096 removed outlier: 4.987A pdb=" N ASN B1094 " --> pdb=" O ALA B1090 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG B1095 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU B1096 " --> pdb=" O SER B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1132 Processing helix chain 'B' and resid 1144 through 1164 Processing helix chain 'B' and resid 1169 through 1181 removed outlier: 3.961A pdb=" N LYS B1181 " --> pdb=" O CYS B1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1201 Processing helix chain 'B' and resid 1206 through 1224 removed outlier: 3.874A pdb=" N HIS B1213 " --> pdb=" O PHE B1209 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASP B1215 " --> pdb=" O ALA B1211 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B1216 " --> pdb=" O SER B1212 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1244 through 1261 removed outlier: 6.016A pdb=" N LYS B1253 " --> pdb=" O ARG B1249 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B1254 " --> pdb=" O SER B1250 " (cutoff:3.500A) Proline residue: B1257 - end of helix Processing helix chain 'B' and resid 1265 through 1275 Processing helix chain 'B' and resid 1279 through 1285 Processing helix chain 'B' and resid 1287 through 1297 removed outlier: 3.604A pdb=" N ASN B1293 " --> pdb=" O LYS B1289 " (cutoff:3.500A) Proline residue: B1296 - end of helix Processing helix chain 'B' and resid 1306 through 1322 removed outlier: 4.273A pdb=" N GLN B1310 " --> pdb=" O SER B1306 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B1311 " --> pdb=" O GLY B1307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B1312 " --> pdb=" O MET B1308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1328 through 1330 No H-bonds generated for 'chain 'B' and resid 1328 through 1330' Processing helix chain 'B' and resid 1332 through 1338 Processing helix chain 'B' and resid 1340 through 1350 removed outlier: 3.650A pdb=" N THR B1350 " --> pdb=" O GLU B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1383 through 1396 Processing helix chain 'B' and resid 1404 through 1410 Processing helix chain 'B' and resid 1412 through 1428 removed outlier: 3.526A pdb=" N TYR B1415 " --> pdb=" O PRO B1412 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B1418 " --> pdb=" O TYR B1415 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B1419 " --> pdb=" O GLN B1416 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B1422 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B1424 " --> pdb=" O ALA B1421 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B1425 " --> pdb=" O ILE B1422 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B1428 " --> pdb=" O GLN B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1432 through 1452 removed outlier: 3.751A pdb=" N ASP B1452 " --> pdb=" O LEU B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1477 Processing helix chain 'B' and resid 1485 through 1508 Processing helix chain 'B' and resid 1512 through 1514 No H-bonds generated for 'chain 'B' and resid 1512 through 1514' Processing helix chain 'B' and resid 1517 through 1528 Proline residue: B1526 - end of helix Processing helix chain 'B' and resid 1532 through 1546 removed outlier: 3.562A pdb=" N GLN B1537 " --> pdb=" O GLU B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1553 through 1560 removed outlier: 4.055A pdb=" N ILE B1557 " --> pdb=" O GLU B1553 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR B1558 " --> pdb=" O ASN B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1572 through 1582 Processing helix chain 'B' and resid 1590 through 1602 removed outlier: 3.571A pdb=" N SER B1601 " --> pdb=" O PHE B1597 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B1602 " --> pdb=" O LEU B1598 " (cutoff:3.500A) Processing helix chain 'B' and resid 1608 through 1623 removed outlier: 4.481A pdb=" N GLU B1612 " --> pdb=" O THR B1609 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B1621 " --> pdb=" O ARG B1618 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1634 removed outlier: 3.714A pdb=" N VAL B1629 " --> pdb=" O LYS B1625 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B1630 " --> pdb=" O ASP B1626 " (cutoff:3.500A) Processing helix chain 'B' and resid 1639 through 1641 No H-bonds generated for 'chain 'B' and resid 1639 through 1641' Processing helix chain 'B' and resid 1643 through 1658 Processing helix chain 'B' and resid 1664 through 1677 Processing helix chain 'B' and resid 1694 through 1702 removed outlier: 3.525A pdb=" N LEU B1702 " --> pdb=" O LYS B1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 1706 through 1723 removed outlier: 4.470A pdb=" N VAL B1723 " --> pdb=" O ASN B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1742 Processing helix chain 'B' and resid 1744 through 1753 Processing helix chain 'B' and resid 1759 through 1763 Processing helix chain 'B' and resid 1792 through 1795 No H-bonds generated for 'chain 'B' and resid 1792 through 1795' Processing helix chain 'B' and resid 1802 through 1815 Processing helix chain 'B' and resid 1822 through 1833 removed outlier: 3.716A pdb=" N LEU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B1827 " --> pdb=" O ILE B1823 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS B1828 " --> pdb=" O LEU B1824 " (cutoff:3.500A) Proline residue: B1829 - end of helix removed outlier: 3.705A pdb=" N VAL B1833 " --> pdb=" O PRO B1829 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1851 Proline residue: B1843 - end of helix Processing helix chain 'B' and resid 1857 through 1875 removed outlier: 3.644A pdb=" N LEU B1874 " --> pdb=" O PHE B1870 " (cutoff:3.500A) Processing helix chain 'B' and resid 1903 through 1918 removed outlier: 3.655A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1927 through 1932 removed outlier: 3.999A pdb=" N PHE B1932 " --> pdb=" O PHE B1928 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1947 Processing helix chain 'B' and resid 1951 through 1973 Processing helix chain 'B' and resid 1986 through 1996 Processing helix chain 'B' and resid 2001 through 2012 Processing helix chain 'B' and resid 2016 through 2019 Processing helix chain 'B' and resid 2029 through 2038 Processing helix chain 'B' and resid 2042 through 2051 Processing helix chain 'B' and resid 2057 through 2070 Processing helix chain 'B' and resid 2074 through 2087 Processing helix chain 'B' and resid 2093 through 2105 Processing helix chain 'B' and resid 2124 through 2136 Processing helix chain 'B' and resid 2140 through 2159 Processing helix chain 'B' and resid 2166 through 2168 No H-bonds generated for 'chain 'B' and resid 2166 through 2168' Processing helix chain 'B' and resid 2170 through 2190 removed outlier: 3.613A pdb=" N GLU B2187 " --> pdb=" O GLU B2183 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B2188 " --> pdb=" O SER B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2195 through 2211 Processing helix chain 'B' and resid 2217 through 2236 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2244 through 2264 Processing helix chain 'B' and resid 2269 through 2281 removed outlier: 3.624A pdb=" N TYR B2281 " --> pdb=" O GLN B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2290 through 2301 Processing helix chain 'B' and resid 2305 through 2322 Processing helix chain 'B' and resid 2328 through 2348 removed outlier: 4.119A pdb=" N LEU B2332 " --> pdb=" O PRO B2328 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B2333 " --> pdb=" O SER B2329 " (cutoff:3.500A) Processing helix chain 'B' and resid 2353 through 2359 Processing helix chain 'B' and resid 2361 through 2370 Processing helix chain 'B' and resid 2377 through 2405 Processing helix chain 'B' and resid 2408 through 2421 removed outlier: 3.594A pdb=" N LEU B2417 " --> pdb=" O LYS B2413 " (cutoff:3.500A) Processing helix chain 'B' and resid 2437 through 2476 removed outlier: 4.123A pdb=" N GLU B2449 " --> pdb=" O LEU B2445 " (cutoff:3.500A) Processing helix chain 'B' and resid 2481 through 2494 removed outlier: 3.837A pdb=" N LEU B2490 " --> pdb=" O LEU B2487 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B2492 " --> pdb=" O SER B2489 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B2493 " --> pdb=" O LEU B2490 " (cutoff:3.500A) Processing helix chain 'B' and resid 2498 through 2506 Processing helix chain 'B' and resid 2508 through 2510 No H-bonds generated for 'chain 'B' and resid 2508 through 2510' Processing helix chain 'B' and resid 2513 through 2526 Proline residue: B2518 - end of helix removed outlier: 5.257A pdb=" N TYR B2521 " --> pdb=" O PRO B2518 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B2523 " --> pdb=" O MET B2520 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B2525 " --> pdb=" O GLN B2522 " (cutoff:3.500A) Processing helix chain 'B' and resid 2537 through 2551 Processing helix chain 'B' and resid 2553 through 2555 No H-bonds generated for 'chain 'B' and resid 2553 through 2555' Processing helix chain 'B' and resid 2557 through 2564 Processing helix chain 'B' and resid 2568 through 2572 Processing helix chain 'B' and resid 2593 through 2612 removed outlier: 3.964A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2614 through 2632 Processing helix chain 'B' and resid 2637 through 2640 removed outlier: 4.347A pdb=" N THR B2640 " --> pdb=" O GLN B2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2637 through 2640' Processing helix chain 'B' and resid 2652 through 2655 No H-bonds generated for 'chain 'B' and resid 2652 through 2655' Processing helix chain 'B' and resid 2723 through 2740 Processing helix chain 'B' and resid 2743 through 2747 Processing helix chain 'B' and resid 2776 through 2781 Processing helix chain 'B' and resid 2787 through 2791 Processing helix chain 'B' and resid 2798 through 2807 Processing helix chain 'B' and resid 2813 through 2825 Processing helix chain 'B' and resid 2831 through 2838 removed outlier: 3.900A pdb=" N CYS B2835 " --> pdb=" O ARG B2832 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B2836 " --> pdb=" O TYR B2833 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B2837 " --> pdb=" O PHE B2834 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B2838 " --> pdb=" O CYS B2835 " (cutoff:3.500A) Processing helix chain 'B' and resid 2842 through 2866 Processing helix chain 'B' and resid 2873 through 2875 No H-bonds generated for 'chain 'B' and resid 2873 through 2875' Processing helix chain 'B' and resid 2897 through 2899 No H-bonds generated for 'chain 'B' and resid 2897 through 2899' Processing helix chain 'B' and resid 2912 through 2918 removed outlier: 3.772A pdb=" N MET B2918 " --> pdb=" O ILE B2914 " (cutoff:3.500A) Processing helix chain 'B' and resid 2926 through 2940 Processing helix chain 'B' and resid 2942 through 2953 Processing helix chain 'B' and resid 2964 through 2970 Processing helix chain 'B' and resid 3002 through 3018 Processing helix chain 'B' and resid 3028 through 3040 Processing helix chain 'B' and resid 3042 through 3047 removed outlier: 3.731A pdb=" N ARG B3047 " --> pdb=" O LYS B3043 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3052 No H-bonds generated for 'chain 'B' and resid 3050 through 3052' Processing sheet with id= A, first strand: chain 'A' and resid 1060 through 1063 Processing sheet with id= B, first strand: chain 'A' and resid 2757 through 2759 Processing sheet with id= C, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id= D, first strand: chain 'B' and resid 1060 through 1063 Processing sheet with id= E, first strand: chain 'B' and resid 2757 through 2759 Processing sheet with id= F, first strand: chain 'B' and resid 2773 through 2775 2424 hydrogen bonds defined for protein. 6900 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: 23.08 Time building geometry restraints manager: 18.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13991 1.34 - 1.46: 6421 1.46 - 1.58: 24444 1.58 - 1.70: 8 1.70 - 1.82: 450 Bond restraints: 45314 Sorted by residual: bond pdb=" O3A ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O5' ANP B3101 " pdb=" PA ANP B3101 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 45309 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.55: 1026 106.55 - 113.45: 25177 113.45 - 120.34: 16627 120.34 - 127.23: 17958 127.23 - 134.12: 446 Bond angle restraints: 61234 Sorted by residual: angle pdb=" PB ANP B3101 " pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 126.95 108.73 18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" PB ANP A3101 " pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 126.95 108.73 18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C LEU B 409 " pdb=" N VAL B 410 " pdb=" CA VAL B 410 " ideal model delta sigma weight residual 120.24 123.12 -2.88 6.30e-01 2.52e+00 2.09e+01 angle pdb=" C LEU A 409 " pdb=" N VAL A 410 " pdb=" CA VAL A 410 " ideal model delta sigma weight residual 120.24 123.12 -2.88 6.30e-01 2.52e+00 2.09e+01 angle pdb=" CG ARG A1312 " pdb=" CD ARG A1312 " pdb=" NE ARG A1312 " ideal model delta sigma weight residual 112.00 120.14 -8.14 2.20e+00 2.07e-01 1.37e+01 ... (remaining 61229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 23588 17.87 - 35.74: 3022 35.74 - 53.61: 790 53.61 - 71.48: 190 71.48 - 89.36: 82 Dihedral angle restraints: 27672 sinusoidal: 11314 harmonic: 16358 Sorted by residual: dihedral pdb=" CG ARG B1312 " pdb=" CD ARG B1312 " pdb=" NE ARG B1312 " pdb=" CZ ARG B1312 " ideal model delta sinusoidal sigma weight residual 90.00 9.27 80.73 2 1.50e+01 4.44e-03 2.08e+01 dihedral pdb=" CG ARG A1312 " pdb=" CD ARG A1312 " pdb=" NE ARG A1312 " pdb=" CZ ARG A1312 " ideal model delta sinusoidal sigma weight residual 90.00 9.27 80.73 2 1.50e+01 4.44e-03 2.08e+01 dihedral pdb=" CA ASN B1377 " pdb=" C ASN B1377 " pdb=" N PRO B1378 " pdb=" CA PRO B1378 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 27669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6062 0.053 - 0.107: 894 0.107 - 0.160: 64 0.160 - 0.214: 0 0.214 - 0.267: 2 Chirality restraints: 7022 Sorted by residual: chirality pdb=" C3' ANP B3101 " pdb=" C2' ANP B3101 " pdb=" C4' ANP B3101 " pdb=" O3' ANP B3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ILE B2511 " pdb=" N ILE B2511 " pdb=" C ILE B2511 " pdb=" CB ILE B2511 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 7019 not shown) Planarity restraints: 7708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 595 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 596 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 596 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 596 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 595 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 596 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 596 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 596 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B2055 " -0.030 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO B2056 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B2056 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B2056 " -0.026 5.00e-02 4.00e+02 ... (remaining 7705 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 786 2.70 - 3.25: 44424 3.25 - 3.80: 73342 3.80 - 4.35: 93177 4.35 - 4.90: 153305 Nonbonded interactions: 365034 Sorted by model distance: nonbonded pdb=" OH TYR A2969 " pdb=" O2G ANP A3101 " model vdw 2.151 2.440 nonbonded pdb=" OH TYR B2969 " pdb=" O2G ANP B3101 " model vdw 2.151 2.440 nonbonded pdb=" O THR A2142 " pdb=" OG SER A2146 " model vdw 2.186 2.440 nonbonded pdb=" O THR B2142 " pdb=" OG SER B2146 " model vdw 2.186 2.440 nonbonded pdb=" N ASN A 272 " pdb=" OD1 ASN A 272 " model vdw 2.190 2.520 ... (remaining 365029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.260 Check model and map are aligned: 0.670 Set scattering table: 0.400 Process input model: 117.040 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 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 : 0.003 0.144 45314 Z= 0.186 Angle : 0.577 18.216 61234 Z= 0.296 Chirality : 0.036 0.267 7022 Planarity : 0.004 0.051 7708 Dihedral : 17.753 89.356 17004 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.04 % Allowed : 22.52 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.12), residues: 5470 helix: 2.21 (0.09), residues: 3836 sheet: 0.00 (0.58), residues: 66 loop : -0.13 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2104 HIS 0.003 0.001 HIS B 192 PHE 0.018 0.001 PHE A2799 TYR 0.015 0.001 TYR B 959 ARG 0.017 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 586 time to evaluate : 4.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1503 (mmt) cc_final: 0.1042 (mtm) REVERT: A 1063 VAL cc_start: 0.2530 (OUTLIER) cc_final: 0.1947 (p) REVERT: A 1134 MET cc_start: 0.1920 (mtm) cc_final: 0.0913 (ptm) REVERT: A 1322 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4546 (mp) REVERT: A 1540 ASP cc_start: 0.7395 (m-30) cc_final: 0.7177 (t0) REVERT: A 1669 GLU cc_start: 0.7553 (tt0) cc_final: 0.7286 (tm-30) REVERT: A 1701 LYS cc_start: 0.7757 (mmtp) cc_final: 0.7408 (mmtt) REVERT: A 1721 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8516 (t) REVERT: A 1773 LYS cc_start: 0.6605 (tmmt) cc_final: 0.6342 (ttpt) REVERT: A 1991 GLU cc_start: 0.6295 (mt-10) cc_final: 0.6057 (mm-30) REVERT: A 2007 GLU cc_start: 0.7081 (mp0) cc_final: 0.6791 (mm-30) REVERT: A 2034 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7230 (mtp180) REVERT: A 2057 SER cc_start: 0.7913 (m) cc_final: 0.7664 (m) REVERT: A 2141 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6901 (m) REVERT: A 2189 PHE cc_start: 0.7841 (t80) cc_final: 0.7417 (t80) REVERT: A 2232 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7270 (mt-10) REVERT: A 2266 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7832 (mmpt) REVERT: A 2314 GLN cc_start: 0.7258 (mm-40) cc_final: 0.7042 (tm-30) REVERT: A 2315 MET cc_start: 0.7637 (mtp) cc_final: 0.7394 (mtp) REVERT: A 2377 ASP cc_start: 0.6932 (t70) cc_final: 0.6665 (t0) REVERT: A 2378 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6495 (tp30) REVERT: A 2406 LYS cc_start: 0.6817 (mtmt) cc_final: 0.6554 (mmtm) REVERT: A 2529 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.6522 (p) REVERT: A 2531 MET cc_start: 0.5530 (ttm) cc_final: 0.5105 (ttp) REVERT: A 2636 THR cc_start: 0.7464 (t) cc_final: 0.7098 (t) REVERT: A 2670 LYS cc_start: 0.7986 (tppt) cc_final: 0.7780 (tmtt) REVERT: A 2703 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: A 2710 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7289 (ttpp) REVERT: A 2810 LYS cc_start: 0.6882 (mtpt) cc_final: 0.6679 (mppt) REVERT: A 2935 MET cc_start: 0.8457 (tpp) cc_final: 0.7289 (tpp) REVERT: A 2966 LYS cc_start: 0.7102 (ttmt) cc_final: 0.6695 (ttmm) REVERT: A 3004 LYS cc_start: 0.7444 (mttm) cc_final: 0.7019 (ttpt) REVERT: A 3007 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6729 (mt-10) REVERT: B 94 MET cc_start: 0.1507 (mmt) cc_final: 0.1044 (mtm) REVERT: B 1063 VAL cc_start: 0.2538 (OUTLIER) cc_final: 0.1954 (p) REVERT: B 1134 MET cc_start: 0.1913 (mtm) cc_final: 0.0912 (ptm) REVERT: B 1322 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4542 (mp) REVERT: B 1540 ASP cc_start: 0.7409 (m-30) cc_final: 0.7184 (t0) REVERT: B 1669 GLU cc_start: 0.7550 (tt0) cc_final: 0.7284 (tm-30) REVERT: B 1701 LYS cc_start: 0.7750 (mmtp) cc_final: 0.7400 (mmtt) REVERT: B 1721 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8513 (t) REVERT: B 1773 LYS cc_start: 0.6592 (tmmt) cc_final: 0.6320 (ttpt) REVERT: B 1991 GLU cc_start: 0.6284 (mt-10) cc_final: 0.6043 (mm-30) REVERT: B 2007 GLU cc_start: 0.7072 (mp0) cc_final: 0.6780 (mm-30) REVERT: B 2034 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7230 (mtp180) REVERT: B 2057 SER cc_start: 0.7901 (m) cc_final: 0.7654 (m) REVERT: B 2141 SER cc_start: 0.7242 (OUTLIER) cc_final: 0.6900 (m) REVERT: B 2189 PHE cc_start: 0.7838 (t80) cc_final: 0.7418 (t80) REVERT: B 2232 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 2266 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7846 (mmpt) REVERT: B 2314 GLN cc_start: 0.7269 (mm-40) cc_final: 0.7057 (tm-30) REVERT: B 2315 MET cc_start: 0.7640 (mtp) cc_final: 0.7395 (mtp) REVERT: B 2377 ASP cc_start: 0.6933 (t70) cc_final: 0.6666 (t0) REVERT: B 2378 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6528 (tp30) REVERT: B 2406 LYS cc_start: 0.6825 (mtmt) cc_final: 0.6564 (mmtm) REVERT: B 2529 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6526 (p) REVERT: B 2531 MET cc_start: 0.5533 (ttm) cc_final: 0.5106 (ttp) REVERT: B 2636 THR cc_start: 0.7474 (t) cc_final: 0.7108 (t) REVERT: B 2703 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: B 2710 LYS cc_start: 0.7638 (ttmt) cc_final: 0.7295 (ttpp) REVERT: B 2935 MET cc_start: 0.8462 (tpp) cc_final: 0.7292 (tpp) REVERT: B 2966 LYS cc_start: 0.7119 (ttmt) cc_final: 0.6719 (ttmm) REVERT: B 3004 LYS cc_start: 0.7454 (mttm) cc_final: 0.7036 (ttpt) REVERT: B 3007 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6740 (mt-10) outliers start: 150 outliers final: 36 residues processed: 722 average time/residue: 1.5302 time to fit residues: 1369.3935 Evaluate side-chains 483 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 433 time to evaluate : 5.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1576 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2378 GLU Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2703 ASP Chi-restraints excluded: chain A residue 2705 VAL Chi-restraints excluded: chain A residue 2920 ILE Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 917 SER Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1143 THR Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1567 ASP Chi-restraints excluded: chain B residue 1576 ILE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1806 ILE Chi-restraints excluded: chain B residue 1989 LEU Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2378 GLU Chi-restraints excluded: chain B residue 2529 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2698 LEU Chi-restraints excluded: chain B residue 2703 ASP Chi-restraints excluded: chain B residue 2705 VAL Chi-restraints excluded: chain B residue 2920 ILE Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 467 optimal weight: 0.9990 chunk 419 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 434 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 323 optimal weight: 30.0000 chunk 503 optimal weight: 0.0070 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 405 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** A1311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 ASN A1653 GLN A1801 ASN A2038 HIS A2412 ASN ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2881 GLN B 118 GLN B 405 ASN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1116 GLN ** B1311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN B1801 ASN B2038 HIS B2412 ASN ** B2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2881 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45314 Z= 0.182 Angle : 0.512 9.114 61234 Z= 0.256 Chirality : 0.037 0.167 7022 Planarity : 0.004 0.052 7708 Dihedral : 5.455 88.830 6090 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.03 % Allowed : 22.11 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.12), residues: 5470 helix: 2.10 (0.08), residues: 3860 sheet: 0.17 (0.59), residues: 66 loop : -0.08 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2104 HIS 0.005 0.001 HIS B2538 PHE 0.037 0.001 PHE B1265 TYR 0.015 0.001 TYR A1556 ARG 0.006 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 458 time to evaluate : 5.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1669 (mmt) cc_final: 0.1195 (mtm) REVERT: A 1040 MET cc_start: 0.3329 (ptm) cc_final: 0.2982 (ttm) REVERT: A 1134 MET cc_start: 0.2087 (mtm) cc_final: 0.0981 (ptm) REVERT: A 1321 MET cc_start: 0.4160 (pp-130) cc_final: 0.2407 (ttp) REVERT: A 1539 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7508 (mm) REVERT: A 1548 ASP cc_start: 0.7087 (m-30) cc_final: 0.6856 (m-30) REVERT: A 1669 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: A 1701 LYS cc_start: 0.7718 (mmtp) cc_final: 0.7408 (mmtp) REVERT: A 1792 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7374 (mt) REVERT: A 1796 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6888 (mt) REVERT: A 1991 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6115 (mm-30) REVERT: A 2007 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: A 2026 MET cc_start: 0.5436 (OUTLIER) cc_final: 0.5024 (mtp) REVERT: A 2057 SER cc_start: 0.8041 (m) cc_final: 0.7699 (m) REVERT: A 2189 PHE cc_start: 0.7747 (t80) cc_final: 0.7359 (t80) REVERT: A 2237 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6134 (ttpt) REVERT: A 2266 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7840 (mmpt) REVERT: A 2280 GLN cc_start: 0.7586 (tp40) cc_final: 0.7273 (mm110) REVERT: A 2314 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: A 2377 ASP cc_start: 0.7032 (t70) cc_final: 0.6752 (t0) REVERT: A 2378 GLU cc_start: 0.7023 (mp0) cc_final: 0.6560 (tp30) REVERT: A 2531 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.5020 (ttp) REVERT: A 2636 THR cc_start: 0.7469 (t) cc_final: 0.7125 (t) REVERT: A 2642 ARG cc_start: 0.7150 (mpt180) cc_final: 0.6897 (mpt180) REVERT: A 2703 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: A 2935 MET cc_start: 0.8646 (tpp) cc_final: 0.7617 (tpp) REVERT: A 3004 LYS cc_start: 0.7623 (mttm) cc_final: 0.7268 (ttpt) REVERT: A 3007 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6749 (mt-10) REVERT: B 94 MET cc_start: 0.1675 (mmt) cc_final: 0.1198 (mtm) REVERT: B 1040 MET cc_start: 0.3334 (ptm) cc_final: 0.2989 (ttm) REVERT: B 1134 MET cc_start: 0.2083 (mtm) cc_final: 0.0975 (ptm) REVERT: B 1321 MET cc_start: 0.4157 (pp-130) cc_final: 0.2404 (ttp) REVERT: B 1539 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7511 (mm) REVERT: B 1548 ASP cc_start: 0.7088 (m-30) cc_final: 0.6857 (m-30) REVERT: B 1669 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: B 1701 LYS cc_start: 0.7710 (mmtp) cc_final: 0.7401 (mmtp) REVERT: B 1792 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7372 (mt) REVERT: B 1796 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6882 (mt) REVERT: B 1991 GLU cc_start: 0.6354 (mt-10) cc_final: 0.6105 (mm-30) REVERT: B 2007 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: B 2026 MET cc_start: 0.5438 (OUTLIER) cc_final: 0.5026 (mtp) REVERT: B 2057 SER cc_start: 0.8027 (m) cc_final: 0.7687 (m) REVERT: B 2189 PHE cc_start: 0.7745 (t80) cc_final: 0.7358 (t80) REVERT: B 2237 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6145 (ttpt) REVERT: B 2266 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7851 (mmpt) REVERT: B 2280 GLN cc_start: 0.7588 (tp40) cc_final: 0.7282 (mm110) REVERT: B 2314 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: B 2377 ASP cc_start: 0.7027 (t70) cc_final: 0.6751 (t0) REVERT: B 2378 GLU cc_start: 0.7034 (mp0) cc_final: 0.6593 (tp30) REVERT: B 2531 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.5021 (ttp) REVERT: B 2636 THR cc_start: 0.7483 (t) cc_final: 0.7137 (t) REVERT: B 2642 ARG cc_start: 0.7155 (mpt180) cc_final: 0.6902 (mpt180) REVERT: B 2703 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: B 2935 MET cc_start: 0.8658 (tpp) cc_final: 0.7627 (tpp) REVERT: B 3004 LYS cc_start: 0.7632 (mttm) cc_final: 0.7283 (ttpt) REVERT: B 3007 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6759 (mt-10) REVERT: B 3047 ARG cc_start: 0.7054 (mtt90) cc_final: 0.6776 (mtt90) outliers start: 199 outliers final: 60 residues processed: 596 average time/residue: 1.6335 time to fit residues: 1198.9780 Evaluate side-chains 500 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 420 time to evaluate : 5.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1423 CYS Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2146 SER Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2237 LYS Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2531 MET Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2703 ASP Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 966 VAL Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1143 THR Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1423 CYS Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1796 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1989 LEU Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2014 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2146 SER Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2237 LYS Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2531 MET Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2703 ASP Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 279 optimal weight: 30.0000 chunk 156 optimal weight: 0.0370 chunk 418 optimal weight: 10.0000 chunk 342 optimal weight: 0.0070 chunk 138 optimal weight: 4.9990 chunk 503 optimal weight: 4.9990 chunk 544 optimal weight: 1.9990 chunk 448 optimal weight: 0.5980 chunk 499 optimal weight: 0.8980 chunk 171 optimal weight: 0.1980 chunk 404 optimal weight: 5.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 441 GLN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN A1311 GLN A1653 GLN A1801 ASN A2038 HIS A2697 ASN A2881 GLN B 405 ASN B 441 GLN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 ASN B 975 ASN B1311 GLN B1549 ASN B1653 GLN B1801 ASN B2038 HIS B2697 ASN B2881 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 45314 Z= 0.135 Angle : 0.467 8.626 61234 Z= 0.234 Chirality : 0.036 0.138 7022 Planarity : 0.003 0.050 7708 Dihedral : 4.831 89.695 6044 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.50 % Allowed : 22.62 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.12), residues: 5470 helix: 2.17 (0.08), residues: 3858 sheet: 0.22 (0.61), residues: 66 loop : -0.10 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B2104 HIS 0.003 0.001 HIS A2038 PHE 0.022 0.001 PHE B1265 TYR 0.012 0.001 TYR A1556 ARG 0.005 0.000 ARG A2612 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 457 time to evaluate : 5.286 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: A 94 MET cc_start: 0.1765 (mmt) cc_final: 0.1293 (mtm) REVERT: A 125 MET cc_start: 0.2538 (mmt) cc_final: 0.2274 (mmm) REVERT: A 1134 MET cc_start: 0.2092 (mtm) cc_final: 0.0973 (ptm) REVERT: A 1321 MET cc_start: 0.3776 (pp-130) cc_final: 0.2283 (ttp) REVERT: A 1430 ASN cc_start: 0.6297 (OUTLIER) cc_final: 0.5248 (p0) REVERT: A 1432 VAL cc_start: 0.7096 (m) cc_final: 0.6852 (m) REVERT: A 1539 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7503 (mm) REVERT: A 1559 ILE cc_start: 0.8398 (mt) cc_final: 0.8120 (mp) REVERT: A 1669 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: A 1701 LYS cc_start: 0.7819 (mmtp) cc_final: 0.7475 (mmtt) REVERT: A 1706 LYS cc_start: 0.7216 (mmtt) cc_final: 0.6948 (tptt) REVERT: A 1792 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7392 (mt) REVERT: A 1991 GLU cc_start: 0.6330 (mt-10) cc_final: 0.6069 (mm-30) REVERT: A 2007 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: A 2014 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: A 2026 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5132 (mtp) REVERT: A 2028 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7270 (tp-100) REVERT: A 2057 SER cc_start: 0.7964 (m) cc_final: 0.7644 (m) REVERT: A 2061 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7058 (mt0) REVERT: A 2189 PHE cc_start: 0.7549 (t80) cc_final: 0.7118 (t80) REVERT: A 2197 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6597 (mt0) REVERT: A 2266 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7944 (mmpt) REVERT: A 2280 GLN cc_start: 0.7556 (tp40) cc_final: 0.7246 (mm110) REVERT: A 2314 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: A 2377 ASP cc_start: 0.6870 (t70) cc_final: 0.6588 (t0) REVERT: A 2378 GLU cc_start: 0.6975 (mp0) cc_final: 0.6554 (tp30) REVERT: A 2531 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.4727 (tpp) REVERT: A 2636 THR cc_start: 0.7473 (t) cc_final: 0.7132 (t) REVERT: A 2703 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: A 2806 MET cc_start: 0.7136 (mtp) cc_final: 0.6712 (mtp) REVERT: A 2935 MET cc_start: 0.8651 (tpp) cc_final: 0.7776 (tpp) REVERT: A 3004 LYS cc_start: 0.7625 (mttm) cc_final: 0.7278 (ttpt) REVERT: A 3007 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6755 (mt-10) REVERT: B 94 MET cc_start: 0.1767 (mmt) cc_final: 0.1294 (mtm) REVERT: B 125 MET cc_start: 0.2537 (mmt) cc_final: 0.2274 (mmm) REVERT: B 1134 MET cc_start: 0.2089 (mtm) cc_final: 0.0967 (ptm) REVERT: B 1321 MET cc_start: 0.3776 (pp-130) cc_final: 0.2280 (ttp) REVERT: B 1430 ASN cc_start: 0.6287 (OUTLIER) cc_final: 0.5237 (p0) REVERT: B 1432 VAL cc_start: 0.7061 (m) cc_final: 0.6819 (m) REVERT: B 1539 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7506 (mm) REVERT: B 1669 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: B 1701 LYS cc_start: 0.7813 (mmtp) cc_final: 0.7468 (mmtt) REVERT: B 1706 LYS cc_start: 0.7212 (mmtt) cc_final: 0.6942 (tptt) REVERT: B 1792 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7390 (mt) REVERT: B 1991 GLU cc_start: 0.6324 (mt-10) cc_final: 0.6059 (mm-30) REVERT: B 2007 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6784 (mm-30) REVERT: B 2026 MET cc_start: 0.5548 (OUTLIER) cc_final: 0.5117 (mtp) REVERT: B 2028 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7272 (tp-100) REVERT: B 2057 SER cc_start: 0.7949 (m) cc_final: 0.7631 (m) REVERT: B 2061 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: B 2189 PHE cc_start: 0.7547 (t80) cc_final: 0.7116 (t80) REVERT: B 2197 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6591 (mt0) REVERT: B 2266 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7956 (mmpt) REVERT: B 2280 GLN cc_start: 0.7560 (tp40) cc_final: 0.7258 (mm110) REVERT: B 2314 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: B 2377 ASP cc_start: 0.6868 (t70) cc_final: 0.6590 (t0) REVERT: B 2378 GLU cc_start: 0.6987 (mp0) cc_final: 0.6587 (tp30) REVERT: B 2531 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.4734 (tpp) REVERT: B 2636 THR cc_start: 0.7489 (t) cc_final: 0.7145 (t) REVERT: B 2703 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: B 2806 MET cc_start: 0.7131 (mtp) cc_final: 0.6720 (mtp) REVERT: B 2935 MET cc_start: 0.8663 (tpp) cc_final: 0.7785 (tpp) REVERT: B 3004 LYS cc_start: 0.7633 (mttm) cc_final: 0.7292 (ttpt) REVERT: B 3007 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6766 (mt-10) outliers start: 173 outliers final: 56 residues processed: 584 average time/residue: 1.5895 time to fit residues: 1149.9828 Evaluate side-chains 500 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 419 time to evaluate : 4.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1423 CYS Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1655 SER Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2028 GLN Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2531 MET Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2703 ASP Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1190 VAL Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1423 CYS Chi-restraints excluded: chain B residue 1430 ASN Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1453 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1655 SER Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2028 GLN Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2197 GLN Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2235 MET Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2405 MET Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2531 MET Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2697 ASN Chi-restraints excluded: chain B residue 2703 ASP Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 497 optimal weight: 9.9990 chunk 378 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 240 optimal weight: 0.7980 chunk 338 optimal weight: 9.9990 chunk 505 optimal weight: 2.9990 chunk 535 optimal weight: 0.0470 chunk 264 optimal weight: 1.9990 chunk 479 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A 996 HIS A1653 GLN A1719 ASN A2038 HIS ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2697 ASN A2881 GLN ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS B1653 GLN B1719 ASN B2038 HIS B2241 ASN B2697 ASN B2881 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45314 Z= 0.178 Angle : 0.495 11.348 61234 Z= 0.247 Chirality : 0.037 0.190 7022 Planarity : 0.004 0.049 7708 Dihedral : 4.649 86.541 6036 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.24 % Allowed : 23.11 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.12), residues: 5470 helix: 2.08 (0.08), residues: 3872 sheet: 0.19 (0.53), residues: 78 loop : -0.00 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2104 HIS 0.004 0.001 HIS A2538 PHE 0.021 0.001 PHE B2571 TYR 0.015 0.001 TYR B1544 ARG 0.003 0.000 ARG A2613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 447 time to evaluate : 5.074 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 94 MET cc_start: 0.1744 (mmt) cc_final: 0.1284 (mtm) REVERT: A 125 MET cc_start: 0.2201 (OUTLIER) cc_final: 0.1869 (mmm) REVERT: A 753 MET cc_start: 0.2961 (tpp) cc_final: 0.2035 (ttt) REVERT: A 1134 MET cc_start: 0.2019 (mtm) cc_final: 0.0931 (ptm) REVERT: A 1321 MET cc_start: 0.3883 (pp-130) cc_final: 0.2330 (ttp) REVERT: A 1430 ASN cc_start: 0.6377 (OUTLIER) cc_final: 0.5336 (p0) REVERT: A 1539 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7752 (mm) REVERT: A 1669 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: A 1701 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7648 (mmtt) REVERT: A 1706 LYS cc_start: 0.7241 (tmtt) cc_final: 0.6983 (tptt) REVERT: A 1789 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7737 (mm) REVERT: A 1792 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7324 (mt) REVERT: A 1991 GLU cc_start: 0.6410 (mt-10) cc_final: 0.6178 (mm-30) REVERT: A 2007 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6864 (mm-30) REVERT: A 2026 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.5253 (mtp) REVERT: A 2028 GLN cc_start: 0.7567 (tp-100) cc_final: 0.7338 (tp-100) REVERT: A 2057 SER cc_start: 0.8006 (m) cc_final: 0.7690 (m) REVERT: A 2061 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7109 (mt0) REVERT: A 2189 PHE cc_start: 0.7649 (t80) cc_final: 0.7256 (t80) REVERT: A 2197 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6690 (mt0) REVERT: A 2237 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6139 (tmmt) REVERT: A 2280 GLN cc_start: 0.7542 (tp40) cc_final: 0.7280 (mm110) REVERT: A 2314 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: A 2377 ASP cc_start: 0.7041 (t70) cc_final: 0.6761 (t0) REVERT: A 2378 GLU cc_start: 0.6963 (mp0) cc_final: 0.6460 (tp30) REVERT: A 2453 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7217 (ptp90) REVERT: A 2458 ASP cc_start: 0.7138 (m-30) cc_final: 0.6771 (m-30) REVERT: A 2636 THR cc_start: 0.7508 (t) cc_final: 0.7147 (t) REVERT: A 2642 ARG cc_start: 0.7190 (mpt180) cc_final: 0.6883 (mpt180) REVERT: A 2785 ASP cc_start: 0.8093 (p0) cc_final: 0.7806 (p0) REVERT: A 2935 MET cc_start: 0.8696 (tpp) cc_final: 0.7825 (tpp) REVERT: A 3004 LYS cc_start: 0.7678 (mttm) cc_final: 0.7333 (ttpt) REVERT: A 3007 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6543 (mt-10) REVERT: B 94 MET cc_start: 0.1747 (mmt) cc_final: 0.1284 (mtm) REVERT: B 125 MET cc_start: 0.2206 (OUTLIER) cc_final: 0.1872 (mmm) REVERT: B 1134 MET cc_start: 0.2015 (mtm) cc_final: 0.0929 (ptm) REVERT: B 1321 MET cc_start: 0.3887 (pp-130) cc_final: 0.2335 (ttp) REVERT: B 1430 ASN cc_start: 0.6368 (OUTLIER) cc_final: 0.5325 (p0) REVERT: B 1539 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7752 (mm) REVERT: B 1669 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: B 1701 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7643 (mmtt) REVERT: B 1706 LYS cc_start: 0.7236 (tmtt) cc_final: 0.6978 (tptt) REVERT: B 1789 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7747 (mm) REVERT: B 1792 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7323 (mt) REVERT: B 1991 GLU cc_start: 0.6403 (mt-10) cc_final: 0.6169 (mm-30) REVERT: B 2007 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6856 (mm-30) REVERT: B 2026 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5255 (mtp) REVERT: B 2028 GLN cc_start: 0.7572 (tp-100) cc_final: 0.7341 (tp-100) REVERT: B 2057 SER cc_start: 0.7991 (m) cc_final: 0.7677 (m) REVERT: B 2061 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7109 (mt0) REVERT: B 2189 PHE cc_start: 0.7644 (t80) cc_final: 0.7255 (t80) REVERT: B 2197 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6683 (mt0) REVERT: B 2237 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6160 (tmmt) REVERT: B 2280 GLN cc_start: 0.7545 (tp40) cc_final: 0.7290 (mm110) REVERT: B 2314 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: B 2377 ASP cc_start: 0.7037 (t70) cc_final: 0.6759 (t0) REVERT: B 2378 GLU cc_start: 0.6974 (mp0) cc_final: 0.6491 (tp30) REVERT: B 2453 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7219 (ptp90) REVERT: B 2458 ASP cc_start: 0.7161 (m-30) cc_final: 0.6794 (m-30) REVERT: B 2636 THR cc_start: 0.7521 (t) cc_final: 0.7158 (t) REVERT: B 2642 ARG cc_start: 0.7191 (mpt180) cc_final: 0.6888 (mpt180) REVERT: B 2785 ASP cc_start: 0.8085 (p0) cc_final: 0.7797 (p0) REVERT: B 2935 MET cc_start: 0.8708 (tpp) cc_final: 0.7831 (tpp) REVERT: B 3004 LYS cc_start: 0.7687 (mttm) cc_final: 0.7351 (ttpt) REVERT: B 3007 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6552 (mt-10) outliers start: 160 outliers final: 66 residues processed: 549 average time/residue: 1.6056 time to fit residues: 1092.3212 Evaluate side-chains 516 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 426 time to evaluate : 4.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1423 CYS Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1655 SER Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2146 SER Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2237 LYS Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2831 PHE Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1423 CYS Chi-restraints excluded: chain B residue 1430 ASN Chi-restraints excluded: chain B residue 1453 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1655 SER Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1789 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2146 SER Chi-restraints excluded: chain B residue 2197 GLN Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2237 LYS Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2831 PHE Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 445 optimal weight: 2.9990 chunk 303 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 398 optimal weight: 0.7980 chunk 220 optimal weight: 0.9990 chunk 456 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 273 optimal weight: 0.9980 chunk 480 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 354 HIS ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN A1653 GLN A2241 ASN ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2697 ASN A2881 GLN B 42 HIS B 354 HIS B 405 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 ASN B1653 GLN ** B2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2697 ASN B2881 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 45314 Z= 0.154 Angle : 0.482 11.492 61234 Z= 0.238 Chirality : 0.037 0.212 7022 Planarity : 0.003 0.049 7708 Dihedral : 4.507 85.577 6030 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.40 % Allowed : 22.90 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.12), residues: 5470 helix: 2.13 (0.08), residues: 3856 sheet: 0.11 (0.58), residues: 66 loop : -0.08 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2104 HIS 0.004 0.001 HIS A2538 PHE 0.024 0.001 PHE B2571 TYR 0.014 0.001 TYR B1544 ARG 0.006 0.000 ARG A3047 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 445 time to evaluate : 4.906 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 94 MET cc_start: 0.1803 (mmt) cc_final: 0.1296 (mtm) REVERT: A 125 MET cc_start: 0.2353 (OUTLIER) cc_final: 0.2000 (mmm) REVERT: A 753 MET cc_start: 0.3366 (OUTLIER) cc_final: 0.2371 (ttt) REVERT: A 1040 MET cc_start: 0.3327 (ptm) cc_final: 0.3109 (mtt) REVERT: A 1064 MET cc_start: 0.1850 (mpp) cc_final: 0.1213 (ptp) REVERT: A 1134 MET cc_start: 0.1633 (mtm) cc_final: 0.0692 (ptm) REVERT: A 1321 MET cc_start: 0.3857 (pp-130) cc_final: 0.2335 (ttp) REVERT: A 1430 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.5378 (p0) REVERT: A 1669 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: A 1701 LYS cc_start: 0.8024 (mmtp) cc_final: 0.7679 (mmtt) REVERT: A 1706 LYS cc_start: 0.7284 (tmtt) cc_final: 0.7035 (tptt) REVERT: A 1792 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7348 (mt) REVERT: A 1991 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6176 (mm-30) REVERT: A 2007 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: A 2026 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.5297 (mtp) REVERT: A 2028 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7336 (tp-100) REVERT: A 2057 SER cc_start: 0.8006 (m) cc_final: 0.7680 (m) REVERT: A 2061 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: A 2197 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6667 (mt0) REVERT: A 2237 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6143 (tmmt) REVERT: A 2270 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 2280 GLN cc_start: 0.7596 (tp40) cc_final: 0.7301 (mm110) REVERT: A 2314 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: A 2377 ASP cc_start: 0.6994 (t70) cc_final: 0.6709 (t0) REVERT: A 2378 GLU cc_start: 0.6971 (mp0) cc_final: 0.6509 (tp30) REVERT: A 2458 ASP cc_start: 0.7192 (m-30) cc_final: 0.6823 (m-30) REVERT: A 2636 THR cc_start: 0.7679 (t) cc_final: 0.7280 (t) REVERT: A 2642 ARG cc_start: 0.7271 (mpt180) cc_final: 0.6787 (mpt180) REVERT: A 2734 MET cc_start: 0.7335 (tpp) cc_final: 0.7109 (mmp) REVERT: A 2935 MET cc_start: 0.8703 (tpp) cc_final: 0.7977 (tpp) REVERT: A 3004 LYS cc_start: 0.7640 (mttm) cc_final: 0.7267 (ttpt) REVERT: A 3007 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6595 (mt-10) REVERT: B 94 MET cc_start: 0.1808 (mmt) cc_final: 0.1299 (mtm) REVERT: B 125 MET cc_start: 0.2356 (OUTLIER) cc_final: 0.2000 (mmm) REVERT: B 753 MET cc_start: 0.2102 (tpp) cc_final: 0.1433 (ttm) REVERT: B 812 MET cc_start: 0.0490 (ptt) cc_final: 0.0087 (ppp) REVERT: B 1040 MET cc_start: 0.3326 (ptm) cc_final: 0.3115 (mtt) REVERT: B 1064 MET cc_start: 0.1854 (mpp) cc_final: 0.1212 (ptp) REVERT: B 1134 MET cc_start: 0.1630 (mtm) cc_final: 0.0689 (ptm) REVERT: B 1321 MET cc_start: 0.3859 (pp-130) cc_final: 0.2336 (ttp) REVERT: B 1430 ASN cc_start: 0.6429 (OUTLIER) cc_final: 0.5371 (p0) REVERT: B 1669 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: B 1701 LYS cc_start: 0.8022 (mmtp) cc_final: 0.7673 (mmtt) REVERT: B 1706 LYS cc_start: 0.7280 (tmtt) cc_final: 0.7031 (tptt) REVERT: B 1792 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7348 (mt) REVERT: B 1991 GLU cc_start: 0.6434 (mt-10) cc_final: 0.6170 (mm-30) REVERT: B 2007 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6836 (mm-30) REVERT: B 2026 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.5299 (mtp) REVERT: B 2028 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7338 (tp-100) REVERT: B 2057 SER cc_start: 0.7990 (m) cc_final: 0.7666 (m) REVERT: B 2061 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7099 (mt0) REVERT: B 2197 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6662 (mt0) REVERT: B 2237 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6160 (tmmt) REVERT: B 2270 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 2280 GLN cc_start: 0.7599 (tp40) cc_final: 0.7311 (mm110) REVERT: B 2314 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: B 2377 ASP cc_start: 0.6992 (t70) cc_final: 0.6709 (t0) REVERT: B 2378 GLU cc_start: 0.6981 (mp0) cc_final: 0.6541 (tp30) REVERT: B 2458 ASP cc_start: 0.7210 (m-30) cc_final: 0.6839 (m-30) REVERT: B 2636 THR cc_start: 0.7690 (t) cc_final: 0.7292 (t) REVERT: B 2642 ARG cc_start: 0.7271 (mpt180) cc_final: 0.6793 (mpt180) REVERT: B 2734 MET cc_start: 0.7333 (tpp) cc_final: 0.7111 (mmp) REVERT: B 2935 MET cc_start: 0.8712 (tpp) cc_final: 0.7982 (tpp) REVERT: B 3004 LYS cc_start: 0.7651 (mttm) cc_final: 0.7284 (ttpt) outliers start: 168 outliers final: 81 residues processed: 553 average time/residue: 1.6913 time to fit residues: 1145.7718 Evaluate side-chains 525 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 419 time to evaluate : 5.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1423 CYS Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1655 SER Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2028 GLN Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2146 SER Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2237 LYS Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2831 PHE Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1066 LYS Chi-restraints excluded: chain B residue 1108 LEU Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1423 CYS Chi-restraints excluded: chain B residue 1430 ASN Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1453 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1655 SER Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2028 GLN Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2146 SER Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2197 GLN Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2237 LYS Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2357 MET Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2831 PHE Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 180 optimal weight: 0.7980 chunk 482 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 314 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 536 optimal weight: 0.5980 chunk 444 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 281 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1653 GLN A2210 GLN ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2615 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN B2210 GLN ** B2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2615 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 45314 Z= 0.150 Angle : 0.484 12.536 61234 Z= 0.238 Chirality : 0.036 0.206 7022 Planarity : 0.003 0.049 7708 Dihedral : 4.462 83.746 6030 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.98 % Allowed : 23.33 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.12), residues: 5470 helix: 2.17 (0.09), residues: 3858 sheet: 0.22 (0.53), residues: 78 loop : -0.02 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2104 HIS 0.003 0.001 HIS A2538 PHE 0.023 0.001 PHE A2571 TYR 0.014 0.001 TYR B1544 ARG 0.010 0.000 ARG A3047 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 420 time to evaluate : 5.320 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 94 MET cc_start: 0.1856 (mmt) cc_final: 0.1221 (mtp) REVERT: A 125 MET cc_start: 0.2361 (OUTLIER) cc_final: 0.1990 (mmm) REVERT: A 617 MET cc_start: 0.1456 (pp-130) cc_final: 0.0645 (mtt) REVERT: A 753 MET cc_start: 0.3211 (OUTLIER) cc_final: 0.2221 (ttt) REVERT: A 1064 MET cc_start: 0.1720 (mpp) cc_final: 0.0994 (ptp) REVERT: A 1134 MET cc_start: 0.1548 (mtm) cc_final: 0.0724 (ptm) REVERT: A 1321 MET cc_start: 0.3869 (pp-130) cc_final: 0.2350 (ttp) REVERT: A 1669 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 1701 LYS cc_start: 0.8078 (mmtp) cc_final: 0.7734 (mmtt) REVERT: A 1706 LYS cc_start: 0.7293 (tmtt) cc_final: 0.7051 (tptt) REVERT: A 1789 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7725 (mm) REVERT: A 1792 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7322 (mt) REVERT: A 1991 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6154 (mm-30) REVERT: A 2007 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6841 (mm-30) REVERT: A 2026 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5355 (mtp) REVERT: A 2057 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7682 (m) REVERT: A 2061 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: A 2189 PHE cc_start: 0.7719 (t80) cc_final: 0.7408 (t80) REVERT: A 2197 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6657 (mt0) REVERT: A 2237 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6167 (tmmt) REVERT: A 2270 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 2280 GLN cc_start: 0.7585 (tp40) cc_final: 0.7296 (mm110) REVERT: A 2314 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: A 2377 ASP cc_start: 0.6908 (t70) cc_final: 0.6623 (t0) REVERT: A 2378 GLU cc_start: 0.6986 (mp0) cc_final: 0.6507 (tp30) REVERT: A 2458 ASP cc_start: 0.7207 (m-30) cc_final: 0.6833 (m-30) REVERT: A 2531 MET cc_start: 0.5690 (ttp) cc_final: 0.5290 (ttt) REVERT: A 2618 ARG cc_start: 0.7307 (ttp-110) cc_final: 0.7088 (ttm110) REVERT: A 2636 THR cc_start: 0.7700 (t) cc_final: 0.7322 (t) REVERT: A 2734 MET cc_start: 0.7357 (tpp) cc_final: 0.7118 (mmp) REVERT: A 2821 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7257 (mmt) REVERT: A 2935 MET cc_start: 0.8689 (tpp) cc_final: 0.7879 (tpp) REVERT: A 3004 LYS cc_start: 0.7679 (mttm) cc_final: 0.7278 (ttpt) REVERT: A 3007 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6561 (mt-10) REVERT: B 94 MET cc_start: 0.1860 (mmt) cc_final: 0.1222 (mtp) REVERT: B 125 MET cc_start: 0.2364 (OUTLIER) cc_final: 0.1991 (mmm) REVERT: B 617 MET cc_start: 0.1450 (pp-130) cc_final: 0.0637 (mtt) REVERT: B 753 MET cc_start: 0.1874 (tpp) cc_final: 0.1231 (ttm) REVERT: B 812 MET cc_start: 0.0432 (ptt) cc_final: -0.0162 (ppp) REVERT: B 1064 MET cc_start: 0.1725 (mpp) cc_final: 0.0992 (ptp) REVERT: B 1134 MET cc_start: 0.1545 (mtm) cc_final: 0.0724 (ptm) REVERT: B 1321 MET cc_start: 0.3874 (pp-130) cc_final: 0.2351 (ttp) REVERT: B 1669 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: B 1701 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7726 (mmtt) REVERT: B 1706 LYS cc_start: 0.7287 (tmtt) cc_final: 0.7045 (tptt) REVERT: B 1789 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7734 (mm) REVERT: B 1792 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7324 (mt) REVERT: B 1991 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6143 (mm-30) REVERT: B 2007 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6831 (mm-30) REVERT: B 2026 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5356 (mtp) REVERT: B 2057 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7668 (m) REVERT: B 2061 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: B 2189 PHE cc_start: 0.7717 (t80) cc_final: 0.7407 (t80) REVERT: B 2197 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6653 (mt0) REVERT: B 2237 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6183 (tmmt) REVERT: B 2270 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8537 (mp) REVERT: B 2280 GLN cc_start: 0.7589 (tp40) cc_final: 0.7307 (mm110) REVERT: B 2314 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: B 2377 ASP cc_start: 0.6908 (t70) cc_final: 0.6624 (t0) REVERT: B 2378 GLU cc_start: 0.6993 (mp0) cc_final: 0.6538 (tp30) REVERT: B 2458 ASP cc_start: 0.7223 (m-30) cc_final: 0.6854 (m-30) REVERT: B 2531 MET cc_start: 0.5691 (ttp) cc_final: 0.5292 (ttt) REVERT: B 2618 ARG cc_start: 0.7306 (ttp-110) cc_final: 0.7094 (ttm110) REVERT: B 2636 THR cc_start: 0.7713 (t) cc_final: 0.7333 (t) REVERT: B 2734 MET cc_start: 0.7353 (tpp) cc_final: 0.7117 (mmp) REVERT: B 2935 MET cc_start: 0.8716 (tpp) cc_final: 0.7913 (tpp) REVERT: B 3004 LYS cc_start: 0.7686 (mttm) cc_final: 0.7291 (ttpt) outliers start: 147 outliers final: 83 residues processed: 524 average time/residue: 1.6316 time to fit residues: 1056.6998 Evaluate side-chains 522 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 413 time to evaluate : 5.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1655 SER Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1697 THR Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2146 SER Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2237 LYS Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2357 MET Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2705 VAL Chi-restraints excluded: chain A residue 2821 MET Chi-restraints excluded: chain A residue 2831 PHE Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1066 LYS Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1453 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1527 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1655 SER Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1697 THR Chi-restraints excluded: chain B residue 1789 LEU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2146 SER Chi-restraints excluded: chain B residue 2197 GLN Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2237 LYS Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2705 VAL Chi-restraints excluded: chain B residue 2831 PHE Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 516 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 305 optimal weight: 0.8980 chunk 391 optimal weight: 6.9990 chunk 303 optimal weight: 0.0060 chunk 451 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 chunk 533 optimal weight: 0.8980 chunk 334 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 246 optimal weight: 0.0870 overall best weight: 0.5574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1653 GLN A2241 ASN ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1431 ASN B1653 GLN B2241 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 45314 Z= 0.133 Angle : 0.470 10.081 61234 Z= 0.231 Chirality : 0.036 0.221 7022 Planarity : 0.003 0.049 7708 Dihedral : 4.242 82.873 6024 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.96 % Allowed : 23.63 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.12), residues: 5470 helix: 2.21 (0.09), residues: 3860 sheet: 0.22 (0.53), residues: 78 loop : 0.02 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2104 HIS 0.002 0.000 HIS B2872 PHE 0.024 0.001 PHE B2571 TYR 0.017 0.001 TYR A1556 ARG 0.010 0.000 ARG B3047 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 424 time to evaluate : 4.817 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: A 94 MET cc_start: 0.1848 (mmt) cc_final: 0.1258 (mtp) REVERT: A 125 MET cc_start: 0.2351 (OUTLIER) cc_final: 0.1986 (mmm) REVERT: A 617 MET cc_start: 0.1296 (OUTLIER) cc_final: 0.0509 (mtt) REVERT: A 753 MET cc_start: 0.3319 (tpp) cc_final: 0.2313 (ttt) REVERT: A 1134 MET cc_start: 0.1554 (mtm) cc_final: 0.0743 (ptm) REVERT: A 1321 MET cc_start: 0.3877 (pp-130) cc_final: 0.2523 (ttp) REVERT: A 1669 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: A 1701 LYS cc_start: 0.8090 (mmtp) cc_final: 0.7697 (mmtt) REVERT: A 1706 LYS cc_start: 0.7303 (mmtt) cc_final: 0.7064 (tptt) REVERT: A 1774 PHE cc_start: 0.7011 (m-80) cc_final: 0.6779 (m-80) REVERT: A 1792 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7335 (mt) REVERT: A 1796 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6991 (mt) REVERT: A 1991 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6282 (mm-30) REVERT: A 2007 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: A 2026 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.5340 (mtp) REVERT: A 2057 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7683 (m) REVERT: A 2061 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7062 (mt0) REVERT: A 2189 PHE cc_start: 0.7766 (t80) cc_final: 0.7408 (t80) REVERT: A 2197 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6642 (mt0) REVERT: A 2280 GLN cc_start: 0.7572 (tp40) cc_final: 0.7289 (mm110) REVERT: A 2314 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: A 2377 ASP cc_start: 0.6874 (t70) cc_final: 0.6587 (t0) REVERT: A 2378 GLU cc_start: 0.6984 (mp0) cc_final: 0.6492 (tp30) REVERT: A 2453 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7205 (ptp90) REVERT: A 2458 ASP cc_start: 0.7209 (m-30) cc_final: 0.6850 (m-30) REVERT: A 2531 MET cc_start: 0.5978 (ttp) cc_final: 0.5550 (ttt) REVERT: A 2618 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.7030 (ttm110) REVERT: A 2636 THR cc_start: 0.7683 (t) cc_final: 0.7319 (m) REVERT: A 2642 ARG cc_start: 0.7139 (mpt180) cc_final: 0.6937 (mpt180) REVERT: A 2734 MET cc_start: 0.7335 (tpp) cc_final: 0.7066 (mmp) REVERT: A 2935 MET cc_start: 0.8691 (tpp) cc_final: 0.8003 (tpp) REVERT: A 3004 LYS cc_start: 0.7723 (mttm) cc_final: 0.7324 (pttt) REVERT: A 3007 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6559 (mt-10) REVERT: B 94 MET cc_start: 0.1852 (mmt) cc_final: 0.1258 (mtp) REVERT: B 125 MET cc_start: 0.2356 (OUTLIER) cc_final: 0.1990 (mmm) REVERT: B 617 MET cc_start: 0.1296 (OUTLIER) cc_final: 0.0508 (mtt) REVERT: B 753 MET cc_start: 0.1816 (tpp) cc_final: 0.1192 (ttm) REVERT: B 812 MET cc_start: 0.0570 (ptt) cc_final: 0.0040 (ppp) REVERT: B 1134 MET cc_start: 0.1551 (mtm) cc_final: 0.0739 (ptm) REVERT: B 1321 MET cc_start: 0.3879 (pp-130) cc_final: 0.2524 (ttp) REVERT: B 1430 ASN cc_start: 0.6414 (OUTLIER) cc_final: 0.5347 (p0) REVERT: B 1669 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: B 1701 LYS cc_start: 0.8085 (mmtp) cc_final: 0.7690 (mmtt) REVERT: B 1706 LYS cc_start: 0.7296 (mmtt) cc_final: 0.7057 (tptt) REVERT: B 1774 PHE cc_start: 0.7013 (m-80) cc_final: 0.6778 (m-80) REVERT: B 1792 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 1796 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6991 (mt) REVERT: B 1991 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6275 (mm-30) REVERT: B 2007 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: B 2026 MET cc_start: 0.5705 (OUTLIER) cc_final: 0.5342 (mtp) REVERT: B 2057 SER cc_start: 0.7989 (OUTLIER) cc_final: 0.7669 (m) REVERT: B 2061 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7063 (mt0) REVERT: B 2189 PHE cc_start: 0.7764 (t80) cc_final: 0.7407 (t80) REVERT: B 2197 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6634 (mt0) REVERT: B 2280 GLN cc_start: 0.7577 (tp40) cc_final: 0.7302 (mm110) REVERT: B 2314 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: B 2377 ASP cc_start: 0.6875 (t70) cc_final: 0.6589 (t0) REVERT: B 2378 GLU cc_start: 0.6993 (mp0) cc_final: 0.6523 (tp30) REVERT: B 2453 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.7196 (ptp90) REVERT: B 2458 ASP cc_start: 0.7225 (m-30) cc_final: 0.6865 (m-30) REVERT: B 2531 MET cc_start: 0.5977 (ttp) cc_final: 0.5551 (ttt) REVERT: B 2618 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.7033 (ttm110) REVERT: B 2636 THR cc_start: 0.7697 (t) cc_final: 0.7330 (m) REVERT: B 2642 ARG cc_start: 0.7140 (mpt180) cc_final: 0.6940 (mpt180) REVERT: B 2734 MET cc_start: 0.7333 (tpp) cc_final: 0.7070 (mmp) REVERT: B 2935 MET cc_start: 0.8701 (tpp) cc_final: 0.8009 (tpp) REVERT: B 3004 LYS cc_start: 0.7682 (mttm) cc_final: 0.7338 (pttt) outliers start: 146 outliers final: 74 residues processed: 531 average time/residue: 1.6334 time to fit residues: 1073.4936 Evaluate side-chains 510 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 413 time to evaluate : 5.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1655 SER Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2146 SER Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2357 MET Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2594 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2705 VAL Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1430 ASN Chi-restraints excluded: chain B residue 1438 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1527 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1655 SER Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1796 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2057 SER Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2146 SER Chi-restraints excluded: chain B residue 2197 GLN Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2235 MET Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2357 MET Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2594 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2705 VAL Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 330 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 318 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 103 optimal weight: 0.0270 chunk 339 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 chunk 263 optimal weight: 0.4980 chunk 49 optimal weight: 9.9990 chunk 419 optimal weight: 0.8980 overall best weight: 1.2840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1653 GLN ** A2538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN B2241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45314 Z= 0.188 Angle : 0.521 13.581 61234 Z= 0.254 Chirality : 0.038 0.216 7022 Planarity : 0.004 0.048 7708 Dihedral : 4.366 81.476 6024 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.96 % Allowed : 23.63 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.12), residues: 5470 helix: 2.09 (0.09), residues: 3862 sheet: 0.17 (0.52), residues: 78 loop : 0.02 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2104 HIS 0.004 0.001 HIS B2538 PHE 0.027 0.001 PHE A2571 TYR 0.016 0.001 TYR B1544 ARG 0.009 0.000 ARG A3047 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 408 time to evaluate : 4.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.1312 (mmt) cc_final: 0.0822 (mtp) REVERT: A 125 MET cc_start: 0.2549 (OUTLIER) cc_final: 0.2169 (mmm) REVERT: A 617 MET cc_start: 0.1944 (pp-130) cc_final: 0.0850 (mtt) REVERT: A 753 MET cc_start: 0.3116 (OUTLIER) cc_final: 0.2104 (ttt) REVERT: A 923 ILE cc_start: 0.0439 (OUTLIER) cc_final: 0.0213 (tt) REVERT: A 1064 MET cc_start: 0.1836 (mpp) cc_final: 0.1489 (pmm) REVERT: A 1134 MET cc_start: 0.1653 (mtm) cc_final: 0.0831 (ptm) REVERT: A 1321 MET cc_start: 0.3730 (pp-130) cc_final: 0.2447 (ttt) REVERT: A 1430 ASN cc_start: 0.6388 (OUTLIER) cc_final: 0.5309 (p0) REVERT: A 1431 ASN cc_start: 0.6565 (t0) cc_final: 0.6361 (t0) REVERT: A 1669 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: A 1701 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7820 (mmtp) REVERT: A 1706 LYS cc_start: 0.7351 (tmtt) cc_final: 0.7138 (tptt) REVERT: A 1774 PHE cc_start: 0.6973 (m-80) cc_final: 0.6715 (m-80) REVERT: A 1792 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7363 (mt) REVERT: A 1972 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7375 (tmmt) REVERT: A 1991 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6332 (mm-30) REVERT: A 2007 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: A 2057 SER cc_start: 0.8033 (m) cc_final: 0.7711 (m) REVERT: A 2061 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7099 (mt0) REVERT: A 2189 PHE cc_start: 0.7798 (t80) cc_final: 0.7476 (t80) REVERT: A 2237 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6176 (tmmt) REVERT: A 2280 GLN cc_start: 0.7572 (tp40) cc_final: 0.7304 (mm110) REVERT: A 2314 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: A 2315 MET cc_start: 0.8254 (ttm) cc_final: 0.7609 (mtp) REVERT: A 2377 ASP cc_start: 0.7005 (t70) cc_final: 0.6722 (t0) REVERT: A 2378 GLU cc_start: 0.6993 (mp0) cc_final: 0.6489 (tp30) REVERT: A 2379 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7662 (tp) REVERT: A 2458 ASP cc_start: 0.7214 (m-30) cc_final: 0.6858 (m-30) REVERT: A 2531 MET cc_start: 0.6142 (ttp) cc_final: 0.5707 (ttt) REVERT: A 2618 ARG cc_start: 0.7251 (ttp-110) cc_final: 0.6971 (ttm110) REVERT: A 2636 THR cc_start: 0.7855 (t) cc_final: 0.7503 (m) REVERT: A 2642 ARG cc_start: 0.6909 (mpt180) cc_final: 0.6665 (mpt180) REVERT: A 2684 GLN cc_start: 0.8056 (tt0) cc_final: 0.7639 (tt0) REVERT: A 2734 MET cc_start: 0.7444 (tpp) cc_final: 0.7213 (mmp) REVERT: A 2935 MET cc_start: 0.8681 (tpp) cc_final: 0.7870 (tpp) REVERT: A 3004 LYS cc_start: 0.7807 (mttm) cc_final: 0.7468 (pttt) REVERT: A 3007 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6587 (mt-10) REVERT: B 94 MET cc_start: 0.1316 (mmt) cc_final: 0.0824 (mtp) REVERT: B 125 MET cc_start: 0.2552 (OUTLIER) cc_final: 0.2171 (mmm) REVERT: B 617 MET cc_start: 0.1948 (pp-130) cc_final: 0.0850 (mtt) REVERT: B 812 MET cc_start: 0.0835 (ptt) cc_final: 0.0343 (ppp) REVERT: B 1064 MET cc_start: 0.1838 (mpp) cc_final: 0.1489 (pmm) REVERT: B 1134 MET cc_start: 0.1747 (mtm) cc_final: 0.0921 (ptm) REVERT: B 1321 MET cc_start: 0.3735 (pp-130) cc_final: 0.2449 (ttt) REVERT: B 1430 ASN cc_start: 0.6381 (OUTLIER) cc_final: 0.5304 (p0) REVERT: B 1669 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: B 1701 LYS cc_start: 0.8061 (mmtp) cc_final: 0.7813 (mmtp) REVERT: B 1706 LYS cc_start: 0.7344 (tmtt) cc_final: 0.7132 (tptt) REVERT: B 1774 PHE cc_start: 0.6978 (m-80) cc_final: 0.6719 (m-80) REVERT: B 1792 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7367 (mt) REVERT: B 1972 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7370 (tmmt) REVERT: B 1991 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6324 (mm-30) REVERT: B 2007 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6751 (mm-30) REVERT: B 2057 SER cc_start: 0.8018 (m) cc_final: 0.7695 (m) REVERT: B 2061 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7100 (mt0) REVERT: B 2189 PHE cc_start: 0.7796 (t80) cc_final: 0.7476 (t80) REVERT: B 2237 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6191 (tmmt) REVERT: B 2280 GLN cc_start: 0.7575 (tp40) cc_final: 0.7315 (mm110) REVERT: B 2314 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: B 2315 MET cc_start: 0.8259 (ttm) cc_final: 0.7623 (mtp) REVERT: B 2377 ASP cc_start: 0.7003 (t70) cc_final: 0.6719 (t0) REVERT: B 2378 GLU cc_start: 0.7003 (mp0) cc_final: 0.6522 (tp30) REVERT: B 2379 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7685 (tp) REVERT: B 2458 ASP cc_start: 0.7240 (m-30) cc_final: 0.6886 (m-30) REVERT: B 2531 MET cc_start: 0.6142 (ttp) cc_final: 0.5707 (ttt) REVERT: B 2618 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6976 (ttm110) REVERT: B 2636 THR cc_start: 0.7870 (t) cc_final: 0.7512 (m) REVERT: B 2642 ARG cc_start: 0.6909 (mpt180) cc_final: 0.6667 (mpt180) REVERT: B 2684 GLN cc_start: 0.8061 (tt0) cc_final: 0.7644 (tt0) REVERT: B 2734 MET cc_start: 0.7443 (tpp) cc_final: 0.7212 (mmp) REVERT: B 2935 MET cc_start: 0.8692 (tpp) cc_final: 0.7875 (tpp) REVERT: B 3004 LYS cc_start: 0.7814 (mttm) cc_final: 0.7481 (pttt) outliers start: 146 outliers final: 81 residues processed: 509 average time/residue: 1.6790 time to fit residues: 1050.1319 Evaluate side-chains 503 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 400 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1655 SER Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1972 LYS Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2146 SER Chi-restraints excluded: chain A residue 2237 LYS Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2357 MET Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2705 VAL Chi-restraints excluded: chain A residue 2831 PHE Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1430 ASN Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1655 SER Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1972 LYS Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2146 SER Chi-restraints excluded: chain B residue 2235 MET Chi-restraints excluded: chain B residue 2237 LYS Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2357 MET Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2405 MET Chi-restraints excluded: chain B residue 2447 LEU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2705 VAL Chi-restraints excluded: chain B residue 2831 PHE Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 485 optimal weight: 1.9990 chunk 511 optimal weight: 1.9990 chunk 466 optimal weight: 3.9990 chunk 497 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 390 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 449 optimal weight: 0.8980 chunk 470 optimal weight: 0.5980 chunk 495 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 GLN A1653 GLN A2358 GLN ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2881 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1579 GLN B1653 GLN B2241 ASN B2358 GLN ** B2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 45314 Z= 0.149 Angle : 0.505 13.492 61234 Z= 0.243 Chirality : 0.037 0.229 7022 Planarity : 0.003 0.048 7708 Dihedral : 4.304 80.975 6024 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.71 % Allowed : 23.80 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.12), residues: 5470 helix: 2.18 (0.09), residues: 3852 sheet: 0.20 (0.53), residues: 78 loop : -0.03 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2104 HIS 0.003 0.001 HIS A 945 PHE 0.027 0.001 PHE B2571 TYR 0.018 0.001 TYR B1556 ARG 0.009 0.000 ARG A3047 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 411 time to evaluate : 5.575 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: A 94 MET cc_start: 0.1293 (mmt) cc_final: 0.0764 (ptp) REVERT: A 125 MET cc_start: 0.2544 (OUTLIER) cc_final: 0.2184 (mmm) REVERT: A 617 MET cc_start: 0.1754 (OUTLIER) cc_final: 0.0742 (mtt) REVERT: A 753 MET cc_start: 0.3094 (OUTLIER) cc_final: 0.2114 (ttt) REVERT: A 780 MET cc_start: 0.1911 (mmt) cc_final: 0.0931 (tmt) REVERT: A 812 MET cc_start: 0.2309 (ppp) cc_final: 0.1083 (mtm) REVERT: A 923 ILE cc_start: 0.0886 (OUTLIER) cc_final: 0.0583 (tt) REVERT: A 1064 MET cc_start: 0.1796 (mpp) cc_final: 0.1407 (pmm) REVERT: A 1134 MET cc_start: 0.1717 (mtm) cc_final: 0.1076 (ptp) REVERT: A 1321 MET cc_start: 0.3229 (pp-130) cc_final: 0.2014 (ttp) REVERT: A 1430 ASN cc_start: 0.6404 (OUTLIER) cc_final: 0.5336 (p0) REVERT: A 1669 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: A 1701 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7702 (mmtt) REVERT: A 1774 PHE cc_start: 0.6973 (m-80) cc_final: 0.6717 (m-80) REVERT: A 1776 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5571 (mm-30) REVERT: A 1792 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7397 (mt) REVERT: A 1796 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.7006 (mt) REVERT: A 1972 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7331 (tmmt) REVERT: A 1991 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6296 (mm-30) REVERT: A 2007 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6749 (mm-30) REVERT: A 2057 SER cc_start: 0.8020 (m) cc_final: 0.7698 (m) REVERT: A 2061 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7062 (mt0) REVERT: A 2237 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6176 (tmmt) REVERT: A 2280 GLN cc_start: 0.7588 (tp40) cc_final: 0.7313 (mm110) REVERT: A 2314 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: A 2377 ASP cc_start: 0.6904 (t70) cc_final: 0.6614 (t0) REVERT: A 2378 GLU cc_start: 0.6988 (mp0) cc_final: 0.6503 (tp30) REVERT: A 2379 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7636 (tp) REVERT: A 2458 ASP cc_start: 0.7243 (m-30) cc_final: 0.6872 (m-30) REVERT: A 2531 MET cc_start: 0.6171 (ttp) cc_final: 0.5739 (ttt) REVERT: A 2618 ARG cc_start: 0.7272 (ttp-110) cc_final: 0.6979 (ttm110) REVERT: A 2636 THR cc_start: 0.7855 (t) cc_final: 0.7505 (m) REVERT: A 2684 GLN cc_start: 0.8037 (tt0) cc_final: 0.7632 (tt0) REVERT: A 2734 MET cc_start: 0.7387 (tpp) cc_final: 0.7158 (mmp) REVERT: A 2935 MET cc_start: 0.8681 (tpp) cc_final: 0.7891 (tpp) REVERT: A 3004 LYS cc_start: 0.7846 (mttm) cc_final: 0.7419 (pttt) REVERT: B 94 MET cc_start: 0.1295 (mmt) cc_final: 0.0765 (ptp) REVERT: B 125 MET cc_start: 0.2546 (OUTLIER) cc_final: 0.2186 (mmm) REVERT: B 617 MET cc_start: 0.1753 (OUTLIER) cc_final: 0.0743 (mtt) REVERT: B 753 MET cc_start: 0.1889 (tpp) cc_final: 0.1289 (ttm) REVERT: B 780 MET cc_start: 0.1911 (mmt) cc_final: 0.0937 (tmt) REVERT: B 812 MET cc_start: 0.0774 (ptt) cc_final: 0.0399 (ppp) REVERT: B 1064 MET cc_start: 0.1793 (mpp) cc_final: 0.1404 (pmm) REVERT: B 1321 MET cc_start: 0.3233 (pp-130) cc_final: 0.2013 (ttp) REVERT: B 1430 ASN cc_start: 0.6437 (OUTLIER) cc_final: 0.5399 (p0) REVERT: B 1669 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: B 1701 LYS cc_start: 0.8090 (mmtp) cc_final: 0.7694 (mmtt) REVERT: B 1774 PHE cc_start: 0.6974 (m-80) cc_final: 0.6720 (m-80) REVERT: B 1776 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5569 (mm-30) REVERT: B 1792 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7401 (mt) REVERT: B 1796 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.7002 (mt) REVERT: B 1991 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6288 (mm-30) REVERT: B 2007 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6741 (mm-30) REVERT: B 2057 SER cc_start: 0.8003 (m) cc_final: 0.7683 (m) REVERT: B 2061 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7061 (mt0) REVERT: B 2237 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6192 (tmmt) REVERT: B 2280 GLN cc_start: 0.7590 (tp40) cc_final: 0.7324 (mm110) REVERT: B 2314 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: B 2377 ASP cc_start: 0.6906 (t70) cc_final: 0.6616 (t0) REVERT: B 2378 GLU cc_start: 0.6998 (mp0) cc_final: 0.6537 (tp30) REVERT: B 2379 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7661 (tp) REVERT: B 2458 ASP cc_start: 0.7258 (m-30) cc_final: 0.6885 (m-30) REVERT: B 2531 MET cc_start: 0.6172 (ttp) cc_final: 0.5741 (ttt) REVERT: B 2618 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6983 (ttm110) REVERT: B 2636 THR cc_start: 0.7871 (t) cc_final: 0.7512 (m) REVERT: B 2684 GLN cc_start: 0.8042 (tt0) cc_final: 0.7637 (tt0) REVERT: B 2734 MET cc_start: 0.7385 (tpp) cc_final: 0.7159 (mmp) REVERT: B 2935 MET cc_start: 0.8692 (tpp) cc_final: 0.7901 (tpp) REVERT: B 3004 LYS cc_start: 0.7771 (mttm) cc_final: 0.7344 (pttt) outliers start: 134 outliers final: 79 residues processed: 502 average time/residue: 1.6623 time to fit residues: 1027.8525 Evaluate side-chains 507 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 401 time to evaluate : 5.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1655 SER Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1776 GLU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1972 LYS Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2146 SER Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2237 LYS Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2357 MET Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2705 VAL Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1430 ASN Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1453 ILE Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1655 SER Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1776 GLU Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1796 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2146 SER Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2235 MET Chi-restraints excluded: chain B residue 2237 LYS Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2357 MET Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2405 MET Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2705 VAL Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 326 optimal weight: 5.9990 chunk 526 optimal weight: 1.9990 chunk 321 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 365 optimal weight: 10.0000 chunk 551 optimal weight: 2.9990 chunk 507 optimal weight: 0.6980 chunk 439 optimal weight: 0.2980 chunk 45 optimal weight: 0.0020 chunk 339 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2881 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45314 Z= 0.164 Angle : 0.518 13.158 61234 Z= 0.249 Chirality : 0.038 0.250 7022 Planarity : 0.003 0.048 7708 Dihedral : 4.317 79.717 6024 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.35 % Allowed : 24.28 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.12), residues: 5470 helix: 2.14 (0.09), residues: 3864 sheet: 0.19 (0.53), residues: 78 loop : -0.01 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B2104 HIS 0.003 0.001 HIS A 993 PHE 0.026 0.001 PHE A2571 TYR 0.023 0.001 TYR B 980 ARG 0.010 0.000 ARG A3047 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10940 Ramachandran restraints generated. 5470 Oldfield, 0 Emsley, 5470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 405 time to evaluate : 4.839 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: A 94 MET cc_start: 0.1387 (mmt) cc_final: 0.0854 (ptp) REVERT: A 125 MET cc_start: 0.2433 (OUTLIER) cc_final: 0.2083 (mmm) REVERT: A 617 MET cc_start: 0.1883 (OUTLIER) cc_final: 0.0804 (mtt) REVERT: A 753 MET cc_start: 0.3099 (OUTLIER) cc_final: 0.2124 (ttt) REVERT: A 780 MET cc_start: 0.1902 (mmt) cc_final: 0.0921 (tmt) REVERT: A 812 MET cc_start: 0.2289 (ppp) cc_final: 0.1178 (mtm) REVERT: A 923 ILE cc_start: 0.1109 (OUTLIER) cc_final: 0.0817 (tt) REVERT: A 1064 MET cc_start: 0.1888 (mpp) cc_final: 0.1444 (pmm) REVERT: A 1134 MET cc_start: 0.1737 (mtm) cc_final: 0.0846 (ptm) REVERT: A 1321 MET cc_start: 0.3295 (pp-130) cc_final: 0.2050 (ttp) REVERT: A 1430 ASN cc_start: 0.6497 (OUTLIER) cc_final: 0.5463 (p0) REVERT: A 1669 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: A 1701 LYS cc_start: 0.8078 (mmtp) cc_final: 0.7696 (mmtt) REVERT: A 1774 PHE cc_start: 0.6977 (m-80) cc_final: 0.6708 (m-80) REVERT: A 1792 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7405 (mt) REVERT: A 1796 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7023 (mt) REVERT: A 1972 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7330 (tmmt) REVERT: A 1991 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6297 (mm-30) REVERT: A 2007 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6753 (mm-30) REVERT: A 2057 SER cc_start: 0.8024 (m) cc_final: 0.7769 (m) REVERT: A 2237 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6173 (tmmt) REVERT: A 2280 GLN cc_start: 0.7568 (tp40) cc_final: 0.7306 (mm110) REVERT: A 2314 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: A 2315 MET cc_start: 0.8251 (ttm) cc_final: 0.7636 (mtp) REVERT: A 2377 ASP cc_start: 0.6916 (t70) cc_final: 0.6627 (t0) REVERT: A 2378 GLU cc_start: 0.6992 (mp0) cc_final: 0.6495 (tp30) REVERT: A 2379 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7639 (tp) REVERT: A 2453 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.7145 (ptp90) REVERT: A 2458 ASP cc_start: 0.7235 (m-30) cc_final: 0.6881 (m-30) REVERT: A 2531 MET cc_start: 0.6159 (ttp) cc_final: 0.5738 (ttt) REVERT: A 2618 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.6974 (ttm110) REVERT: A 2636 THR cc_start: 0.7866 (t) cc_final: 0.7516 (m) REVERT: A 2684 GLN cc_start: 0.8033 (tt0) cc_final: 0.7619 (tt0) REVERT: A 2734 MET cc_start: 0.7424 (tpp) cc_final: 0.7198 (mmp) REVERT: A 2935 MET cc_start: 0.8685 (tpp) cc_final: 0.7900 (tpp) REVERT: A 2965 LEU cc_start: 0.7944 (tp) cc_final: 0.7730 (tm) REVERT: A 3004 LYS cc_start: 0.7773 (mttm) cc_final: 0.7341 (pttt) REVERT: B 94 MET cc_start: 0.1386 (mmt) cc_final: 0.0852 (ptp) REVERT: B 125 MET cc_start: 0.2562 (OUTLIER) cc_final: 0.2177 (mmm) REVERT: B 617 MET cc_start: 0.1885 (OUTLIER) cc_final: 0.0806 (mtt) REVERT: B 753 MET cc_start: 0.1887 (tpp) cc_final: 0.1290 (ttm) REVERT: B 780 MET cc_start: 0.1902 (mmt) cc_final: 0.0926 (tmt) REVERT: B 812 MET cc_start: 0.0670 (ptt) cc_final: 0.0381 (ppp) REVERT: B 1064 MET cc_start: 0.1884 (mpp) cc_final: 0.1443 (pmm) REVERT: B 1321 MET cc_start: 0.3293 (pp-130) cc_final: 0.2042 (ttp) REVERT: B 1430 ASN cc_start: 0.6491 (OUTLIER) cc_final: 0.5456 (p0) REVERT: B 1669 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: B 1701 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7690 (mmtt) REVERT: B 1774 PHE cc_start: 0.6984 (m-80) cc_final: 0.6712 (m-80) REVERT: B 1792 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7409 (mt) REVERT: B 1796 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7019 (mt) REVERT: B 1972 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7326 (tmmt) REVERT: B 1991 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6291 (mm-30) REVERT: B 2007 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: B 2057 SER cc_start: 0.8009 (m) cc_final: 0.7694 (m) REVERT: B 2061 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7070 (mt0) REVERT: B 2237 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6186 (tmmt) REVERT: B 2280 GLN cc_start: 0.7571 (tp40) cc_final: 0.7315 (mm110) REVERT: B 2314 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: B 2315 MET cc_start: 0.8253 (ttm) cc_final: 0.7652 (mtp) REVERT: B 2377 ASP cc_start: 0.6918 (t70) cc_final: 0.6629 (t0) REVERT: B 2378 GLU cc_start: 0.7001 (mp0) cc_final: 0.6527 (tp30) REVERT: B 2379 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7663 (tp) REVERT: B 2453 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.7155 (ptp90) REVERT: B 2458 ASP cc_start: 0.7235 (m-30) cc_final: 0.6887 (m-30) REVERT: B 2531 MET cc_start: 0.6160 (ttp) cc_final: 0.5738 (ttt) REVERT: B 2618 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.6979 (ttm110) REVERT: B 2636 THR cc_start: 0.7872 (t) cc_final: 0.7517 (m) REVERT: B 2684 GLN cc_start: 0.8039 (tt0) cc_final: 0.7625 (tt0) REVERT: B 2734 MET cc_start: 0.7425 (tpp) cc_final: 0.7199 (mmp) REVERT: B 2935 MET cc_start: 0.8695 (tpp) cc_final: 0.7905 (tpp) REVERT: B 2965 LEU cc_start: 0.7970 (tp) cc_final: 0.7754 (tm) REVERT: B 3004 LYS cc_start: 0.7779 (mttm) cc_final: 0.7356 (pttt) outliers start: 116 outliers final: 84 residues processed: 482 average time/residue: 1.7487 time to fit residues: 1037.7288 Evaluate side-chains 504 residues out of total 5040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 395 time to evaluate : 4.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1266 ASP Chi-restraints excluded: chain A residue 1380 HIS Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1430 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1503 GLN Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1655 SER Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 1796 ILE Chi-restraints excluded: chain A residue 1801 ASN Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1972 LYS Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 2007 GLU Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2107 MET Chi-restraints excluded: chain A residue 2141 SER Chi-restraints excluded: chain A residue 2146 SER Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2237 LYS Chi-restraints excluded: chain A residue 2288 VAL Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2306 SER Chi-restraints excluded: chain A residue 2314 GLN Chi-restraints excluded: chain A residue 2357 MET Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2674 THR Chi-restraints excluded: chain A residue 2705 VAL Chi-restraints excluded: chain A residue 2831 PHE Chi-restraints excluded: chain A residue 2858 THR Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 2968 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1266 ASP Chi-restraints excluded: chain B residue 1380 HIS Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1430 ASN Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1503 GLN Chi-restraints excluded: chain B residue 1608 LEU Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1655 SER Chi-restraints excluded: chain B residue 1669 GLU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1792 ILE Chi-restraints excluded: chain B residue 1796 ILE Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1972 LYS Chi-restraints excluded: chain B residue 1997 THR Chi-restraints excluded: chain B residue 2007 GLU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2061 GLN Chi-restraints excluded: chain B residue 2107 MET Chi-restraints excluded: chain B residue 2141 SER Chi-restraints excluded: chain B residue 2146 SER Chi-restraints excluded: chain B residue 2235 MET Chi-restraints excluded: chain B residue 2237 LYS Chi-restraints excluded: chain B residue 2288 VAL Chi-restraints excluded: chain B residue 2289 SER Chi-restraints excluded: chain B residue 2306 SER Chi-restraints excluded: chain B residue 2314 GLN Chi-restraints excluded: chain B residue 2357 MET Chi-restraints excluded: chain B residue 2379 LEU Chi-restraints excluded: chain B residue 2405 MET Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2666 THR Chi-restraints excluded: chain B residue 2674 THR Chi-restraints excluded: chain B residue 2705 VAL Chi-restraints excluded: chain B residue 2831 PHE Chi-restraints excluded: chain B residue 2858 THR Chi-restraints excluded: chain B residue 2952 LEU Chi-restraints excluded: chain B residue 2968 LEU Chi-restraints excluded: chain B residue 3024 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 349 optimal weight: 5.9990 chunk 468 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 405 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 440 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 452 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 414 GLN ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 414 GLN ** B 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2881 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.256439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.211820 restraints weight = 54135.793| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.01 r_work: 0.4072 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 45314 Z= 0.160 Angle : 0.514 12.673 61234 Z= 0.248 Chirality : 0.037 0.225 7022 Planarity : 0.003 0.048 7708 Dihedral : 4.305 78.659 6024 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.41 % Allowed : 24.30 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.12), residues: 5470 helix: 2.15 (0.09), residues: 3862 sheet: 0.19 (0.53), residues: 78 loop : -0.02 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2104 HIS 0.005 0.001 HIS A 945 PHE 0.018 0.001 PHE A1381 TYR 0.019 0.001 TYR B 980 ARG 0.011 0.000 ARG A3047 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17161.94 seconds wall clock time: 308 minutes 32.66 seconds (18512.66 seconds total)