Starting phenix.real_space_refine on Mon Mar 25 06:46:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liv_23386/03_2024/7liv_23386.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liv_23386/03_2024/7liv_23386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liv_23386/03_2024/7liv_23386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liv_23386/03_2024/7liv_23386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liv_23386/03_2024/7liv_23386.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7liv_23386/03_2024/7liv_23386.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 278 5.16 5 C 29942 2.51 5 N 8257 2.21 5 O 8581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 2": "OE1" <-> "OE2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 110": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "J ARG 212": "NH1" <-> "NH2" Residue "J ARG 234": "NH1" <-> "NH2" Residue "J ARG 373": "NH1" <-> "NH2" Residue "J TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 433": "NH1" <-> "NH2" Residue "J ARG 477": "NH1" <-> "NH2" Residue "J GLU 511": "OE1" <-> "OE2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "J ARG 574": "NH1" <-> "NH2" Residue "J ARG 642": "NH1" <-> "NH2" Residue "J GLU 764": "OE1" <-> "OE2" Residue "J ARG 772": "NH1" <-> "NH2" Residue "J ARG 904": "NH1" <-> "NH2" Residue "J ARG 941": "NH1" <-> "NH2" Residue "J GLU 982": "OE1" <-> "OE2" Residue "J ARG 993": "NH1" <-> "NH2" Residue "J ARG 1132": "NH1" <-> "NH2" Residue "J ARG 1251": "NH1" <-> "NH2" Residue "J ARG 1288": "NH1" <-> "NH2" Residue "J GLU 1305": "OE1" <-> "OE2" Residue "A GLU 2": "OE1" <-> "OE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 633": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A ARG 772": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ARG 904": "NH1" <-> "NH2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A GLU 982": "OE1" <-> "OE2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "A ARG 1251": "NH1" <-> "NH2" Residue "A ARG 1288": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C ARG 421": "NH1" <-> "NH2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C GLU 511": "OE1" <-> "OE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 642": "NH1" <-> "NH2" Residue "C GLU 764": "OE1" <-> "OE2" Residue "C ARG 772": "NH1" <-> "NH2" Residue "C ARG 904": "NH1" <-> "NH2" Residue "C ARG 941": "NH1" <-> "NH2" Residue "C ARG 993": "NH1" <-> "NH2" Residue "C ARG 1069": "NH1" <-> "NH2" Residue "C ARG 1123": "NH1" <-> "NH2" Residue "C ARG 1132": "NH1" <-> "NH2" Residue "C ARG 1139": "NH1" <-> "NH2" Residue "C ARG 1251": "NH1" <-> "NH2" Residue "C ARG 1288": "NH1" <-> "NH2" Residue "C GLU 1305": "OE1" <-> "OE2" Residue "C GLU 1334": "OE1" <-> "OE2" Residue "5 ARG 67": "NH1" <-> "NH2" Residue "5 ARG 176": "NH1" <-> "NH2" Residue "5 ARG 190": "NH1" <-> "NH2" Residue "5 ARG 240": "NH1" <-> "NH2" Residue "6 ARG 11": "NH1" <-> "NH2" Residue "6 ARG 64": "NH1" <-> "NH2" Residue "6 ARG 67": "NH1" <-> "NH2" Residue "6 ARG 111": "NH1" <-> "NH2" Residue "6 ARG 190": "NH1" <-> "NH2" Residue "4 ARG 48": "NH1" <-> "NH2" Residue "4 ARG 141": "NH1" <-> "NH2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 78": "NH1" <-> "NH2" Residue "p TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 220": "NH1" <-> "NH2" Residue "q ARG 240": "NH1" <-> "NH2" Residue "r ARG 74": "NH1" <-> "NH2" Residue "r ARG 75": "NH1" <-> "NH2" Residue "r ARG 160": "NH1" <-> "NH2" Residue "r ARG 220": "NH1" <-> "NH2" Residue "r ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47058 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 10681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1348, 10681 Classifications: {'peptide': 1348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1269} Chain breaks: 1 Chain: "A" Number of atoms: 10526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1328, 10526 Classifications: {'peptide': 1328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 77, 'TRANS': 1250} Chain breaks: 2 Chain: "C" Number of atoms: 10681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1348, 10681 Classifications: {'peptide': 1348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1269} Chain breaks: 1 Chain: "5" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "D" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "E" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "p" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2325 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain: "q" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1911 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "r" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2411 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 286} Time building chain proxies: 23.22, per 1000 atoms: 0.49 Number of scatterers: 47058 At special positions: 0 Unit cell: (183.54, 175.49, 169.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 278 16.00 O 8581 8.00 N 8257 7.00 C 29942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS J1292 " - pdb=" SG CYS J1303 " distance=2.03 Simple disulfide: pdb=" SG CYS A1292 " - pdb=" SG CYS A1303 " distance=2.05 Simple disulfide: pdb=" SG CYS C1292 " - pdb=" SG CYS C1303 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.54 Conformation dependent library (CDL) restraints added in 9.1 seconds 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11322 Finding SS restraints... Secondary structure from input PDB file: 255 helices and 46 sheets defined 47.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'J' and resid 69 through 74 Processing helix chain 'J' and resid 133 through 141 Processing helix chain 'J' and resid 148 through 186 removed outlier: 3.771A pdb=" N LEU J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET J 157 " --> pdb=" O ASN J 153 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 199 Processing helix chain 'J' and resid 208 through 226 removed outlier: 3.554A pdb=" N ARG J 212 " --> pdb=" O ASN J 208 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER J 213 " --> pdb=" O ARG J 209 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU J 224 " --> pdb=" O LYS J 220 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 249 Processing helix chain 'J' and resid 265 through 267 No H-bonds generated for 'chain 'J' and resid 265 through 267' Processing helix chain 'J' and resid 276 through 287 removed outlier: 3.872A pdb=" N ILE J 282 " --> pdb=" O ASN J 278 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER J 285 " --> pdb=" O GLN J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 318 removed outlier: 3.628A pdb=" N THR J 314 " --> pdb=" O GLU J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 335 removed outlier: 3.540A pdb=" N LYS J 329 " --> pdb=" O PHE J 325 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA J 330 " --> pdb=" O ASN J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 377 removed outlier: 4.000A pdb=" N LYS J 377 " --> pdb=" O ARG J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 413 removed outlier: 4.207A pdb=" N SER J 412 " --> pdb=" O THR J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 424 Processing helix chain 'J' and resid 442 through 444 No H-bonds generated for 'chain 'J' and resid 442 through 444' Processing helix chain 'J' and resid 445 through 450 Processing helix chain 'J' and resid 451 through 456 removed outlier: 3.740A pdb=" N HIS J 455 " --> pdb=" O HIS J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 468 removed outlier: 3.733A pdb=" N THR J 463 " --> pdb=" O PRO J 459 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG J 467 " --> pdb=" O THR J 463 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY J 468 " --> pdb=" O PHE J 464 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 480 removed outlier: 3.684A pdb=" N GLU J 480 " --> pdb=" O GLN J 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 490 through 500 Proline residue: J 496 - end of helix removed outlier: 4.094A pdb=" N TYR J 499 " --> pdb=" O ILE J 495 " (cutoff:3.500A) Processing helix chain 'J' and resid 508 through 513 Processing helix chain 'J' and resid 528 through 532 Processing helix chain 'J' and resid 557 through 561 removed outlier: 3.914A pdb=" N LEU J 561 " --> pdb=" O ILE J 558 " (cutoff:3.500A) Processing helix chain 'J' and resid 567 through 582 removed outlier: 3.609A pdb=" N GLU J 572 " --> pdb=" O GLY J 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 603 removed outlier: 3.792A pdb=" N LEU J 596 " --> pdb=" O GLU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 608 through 618 removed outlier: 3.753A pdb=" N LEU J 612 " --> pdb=" O GLU J 608 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS J 618 " --> pdb=" O ASP J 614 " (cutoff:3.500A) Processing helix chain 'J' and resid 620 through 642 removed outlier: 3.943A pdb=" N ILE J 627 " --> pdb=" O ALA J 623 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR J 629 " --> pdb=" O LEU J 625 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE J 630 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG J 633 " --> pdb=" O THR J 629 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 660 removed outlier: 3.648A pdb=" N ALA J 658 " --> pdb=" O VAL J 654 " (cutoff:3.500A) Processing helix chain 'J' and resid 661 through 663 No H-bonds generated for 'chain 'J' and resid 661 through 663' Processing helix chain 'J' and resid 667 through 689 removed outlier: 3.769A pdb=" N HIS J 673 " --> pdb=" O GLN J 669 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR J 674 " --> pdb=" O LEU J 670 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA J 689 " --> pdb=" O THR J 685 " (cutoff:3.500A) Processing helix chain 'J' and resid 703 through 708 removed outlier: 3.568A pdb=" N VAL J 707 " --> pdb=" O LEU J 703 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN J 708 " --> pdb=" O SER J 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 703 through 708' Processing helix chain 'J' and resid 753 through 759 Processing helix chain 'J' and resid 774 through 787 removed outlier: 3.562A pdb=" N LYS J 782 " --> pdb=" O TRP J 778 " (cutoff:3.500A) Processing helix chain 'J' and resid 787 through 794 Processing helix chain 'J' and resid 803 through 812 removed outlier: 4.163A pdb=" N VAL J 809 " --> pdb=" O LYS J 805 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP J 810 " --> pdb=" O THR J 806 " (cutoff:3.500A) Processing helix chain 'J' and resid 814 through 819 Processing helix chain 'J' and resid 847 through 854 removed outlier: 3.736A pdb=" N GLN J 851 " --> pdb=" O ALA J 847 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA J 852 " --> pdb=" O ALA J 848 " (cutoff:3.500A) Processing helix chain 'J' and resid 854 through 862 removed outlier: 3.697A pdb=" N GLU J 859 " --> pdb=" O GLU J 855 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU J 860 " --> pdb=" O MET J 856 " (cutoff:3.500A) Processing helix chain 'J' and resid 871 through 881 removed outlier: 4.065A pdb=" N GLU J 878 " --> pdb=" O GLN J 874 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU J 879 " --> pdb=" O ALA J 875 " (cutoff:3.500A) Processing helix chain 'J' and resid 882 through 886 Processing helix chain 'J' and resid 929 through 932 removed outlier: 4.284A pdb=" N GLU J 932 " --> pdb=" O THR J 929 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 929 through 932' Processing helix chain 'J' and resid 945 through 951 Processing helix chain 'J' and resid 953 through 963 removed outlier: 3.668A pdb=" N TYR J 959 " --> pdb=" O ASP J 955 " (cutoff:3.500A) Processing helix chain 'J' and resid 964 through 968 removed outlier: 3.781A pdb=" N ARG J 968 " --> pdb=" O HIS J 965 " (cutoff:3.500A) Processing helix chain 'J' and resid 988 through 996 removed outlier: 4.132A pdb=" N SER J 992 " --> pdb=" O ARG J 988 " (cutoff:3.500A) Processing helix chain 'J' and resid 1001 through 1011 removed outlier: 4.346A pdb=" N LEU J1008 " --> pdb=" O SER J1004 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA J1009 " --> pdb=" O VAL J1005 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1026 removed outlier: 3.755A pdb=" N ALA J1026 " --> pdb=" O LEU J1022 " (cutoff:3.500A) Processing helix chain 'J' and resid 1112 through 1117 Processing helix chain 'J' and resid 1124 through 1136 removed outlier: 3.681A pdb=" N ASP J1128 " --> pdb=" O HIS J1124 " (cutoff:3.500A) Processing helix chain 'J' and resid 1143 through 1154 removed outlier: 4.015A pdb=" N THR J1152 " --> pdb=" O ILE J1148 " (cutoff:3.500A) Processing helix chain 'J' and resid 1206 through 1215 removed outlier: 3.997A pdb=" N LYS J1212 " --> pdb=" O GLU J1208 " (cutoff:3.500A) Processing helix chain 'J' and resid 1230 through 1235 Processing helix chain 'J' and resid 1240 through 1245 Processing helix chain 'J' and resid 1245 through 1250 Processing helix chain 'J' and resid 1262 through 1267 removed outlier: 3.743A pdb=" N PHE J1266 " --> pdb=" O CYS J1262 " (cutoff:3.500A) Processing helix chain 'J' and resid 1267 through 1275 removed outlier: 3.729A pdb=" N ALA J1273 " --> pdb=" O GLU J1269 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN J1275 " --> pdb=" O ILE J1271 " (cutoff:3.500A) Processing helix chain 'J' and resid 1277 through 1288 Processing helix chain 'J' and resid 1313 through 1319 removed outlier: 4.059A pdb=" N LEU J1317 " --> pdb=" O ASN J1313 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J1318 " --> pdb=" O PRO J1314 " (cutoff:3.500A) Processing helix chain 'J' and resid 1329 through 1339 Processing helix chain 'J' and resid 1361 through 1370 removed outlier: 5.070A pdb=" N LEU J1367 " --> pdb=" O GLN J1363 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE J1368 " --> pdb=" O GLN J1364 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER J1370 " --> pdb=" O MET J1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.615A pdb=" N ARG A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.601A pdb=" N TYR A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 186 removed outlier: 3.968A pdb=" N LEU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.547A pdb=" N VAL A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 3.601A pdb=" N SER A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.159A pdb=" N ARG A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.687A pdb=" N LYS A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.982A pdb=" N ALA A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.744A pdb=" N ILE A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.655A pdb=" N ALA A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.525A pdb=" N ALA A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.992A pdb=" N LYS A 377 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 4.288A pdb=" N SER A 412 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.547A pdb=" N CYS A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.818A pdb=" N ARG A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.671A pdb=" N GLU A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 499 Proline residue: A 496 - end of helix removed outlier: 3.784A pdb=" N TYR A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.680A pdb=" N MET A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 590 through 603 Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.918A pdb=" N LEU A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 642 removed outlier: 3.512A pdb=" N PHE A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR A 629 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 633 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 658 removed outlier: 3.914A pdb=" N LEU A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 663 removed outlier: 4.204A pdb=" N ASP A 663 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 689 removed outlier: 3.820A pdb=" N HIS A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.629A pdb=" N VAL A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 703 through 708' Processing helix chain 'A' and resid 753 through 759 Processing helix chain 'A' and resid 774 through 794 removed outlier: 4.555A pdb=" N MET A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 803 through 812 removed outlier: 4.023A pdb=" N VAL A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 847 through 862 removed outlier: 3.714A pdb=" N GLN A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N MET A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 860 " --> pdb=" O MET A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 881 removed outlier: 3.696A pdb=" N GLU A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 929 through 932 removed outlier: 4.486A pdb=" N GLU A 932 " --> pdb=" O THR A 929 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 929 through 932' Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 953 through 963 removed outlier: 3.580A pdb=" N TYR A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 removed outlier: 3.822A pdb=" N ARG A 968 " --> pdb=" O HIS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 998 removed outlier: 4.238A pdb=" N SER A 992 " --> pdb=" O ARG A 988 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1012 removed outlier: 4.268A pdb=" N LEU A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A1009 " --> pdb=" O VAL A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1026 removed outlier: 3.567A pdb=" N LYS A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1117 Processing helix chain 'A' and resid 1124 through 1136 removed outlier: 3.754A pdb=" N ASP A1128 " --> pdb=" O HIS A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1216 removed outlier: 3.775A pdb=" N LYS A1212 " --> pdb=" O GLU A1208 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 3.777A pdb=" N GLN A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1245 Processing helix chain 'A' and resid 1245 through 1250 Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1267 through 1275 removed outlier: 3.747A pdb=" N ALA A1273 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A1275 " --> pdb=" O ILE A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1285 Processing helix chain 'A' and resid 1313 through 1319 removed outlier: 3.813A pdb=" N LEU A1317 " --> pdb=" O ASN A1313 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A1318 " --> pdb=" O PRO A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1339 removed outlier: 3.572A pdb=" N MET A1333 " --> pdb=" O THR A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 removed outlier: 4.849A pdb=" N LEU A1367 " --> pdb=" O GLN A1363 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A1370 " --> pdb=" O MET A1366 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 Processing helix chain 'C' and resid 22 through 29 removed outlier: 3.603A pdb=" N SER C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.532A pdb=" N ALA C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 141 removed outlier: 3.688A pdb=" N TYR C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 186 removed outlier: 3.805A pdb=" N ILE C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET C 157 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 199 Processing helix chain 'C' and resid 208 through 226 removed outlier: 3.922A pdb=" N SER C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.826A pdb=" N ARG C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 249 Processing helix chain 'C' and resid 276 through 287 removed outlier: 3.565A pdb=" N ILE C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.817A pdb=" N ALA C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.722A pdb=" N LYS C 377 " --> pdb=" O ARG C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 441 through 444 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.896A pdb=" N CYS C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 Processing helix chain 'C' and resid 457 through 468 removed outlier: 3.511A pdb=" N THR C 463 " --> pdb=" O PRO C 459 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 467 " --> pdb=" O THR C 463 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 474 No H-bonds generated for 'chain 'C' and resid 472 through 474' Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.713A pdb=" N GLU C 480 " --> pdb=" O GLN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 499 Proline residue: C 496 - end of helix removed outlier: 4.071A pdb=" N TYR C 499 " --> pdb=" O ILE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 557 through 561 removed outlier: 3.650A pdb=" N LEU C 561 " --> pdb=" O ILE C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 582 removed outlier: 3.566A pdb=" N HIS C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 572 " --> pdb=" O GLY C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 603 removed outlier: 3.818A pdb=" N LEU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 618 removed outlier: 3.766A pdb=" N LEU C 612 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS C 618 " --> pdb=" O ASP C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 627 removed outlier: 3.702A pdb=" N PHE C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 626 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 627 " --> pdb=" O ALA C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.615A pdb=" N ARG C 633 " --> pdb=" O THR C 629 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 660 removed outlier: 3.782A pdb=" N LEU C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 658 " --> pdb=" O VAL C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 663 No H-bonds generated for 'chain 'C' and resid 661 through 663' Processing helix chain 'C' and resid 667 through 689 removed outlier: 3.787A pdb=" N HIS C 673 " --> pdb=" O GLN C 669 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 708 removed outlier: 3.541A pdb=" N VAL C 707 " --> pdb=" O LEU C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 760 Processing helix chain 'C' and resid 774 through 787 Processing helix chain 'C' and resid 787 through 794 Processing helix chain 'C' and resid 803 through 812 removed outlier: 3.929A pdb=" N VAL C 809 " --> pdb=" O LYS C 805 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 810 " --> pdb=" O THR C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 847 through 862 removed outlier: 3.726A pdb=" N ALA C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU C 855 " --> pdb=" O GLN C 851 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N MET C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 857 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C 860 " --> pdb=" O MET C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 881 removed outlier: 4.145A pdb=" N GLU C 878 " --> pdb=" O GLN C 874 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 879 " --> pdb=" O ALA C 875 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 881 " --> pdb=" O ARG C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 929 through 932 removed outlier: 4.347A pdb=" N GLU C 932 " --> pdb=" O THR C 929 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 929 through 932' Processing helix chain 'C' and resid 945 through 951 removed outlier: 3.785A pdb=" N ALA C 951 " --> pdb=" O THR C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 963 Processing helix chain 'C' and resid 964 through 968 removed outlier: 3.712A pdb=" N ARG C 968 " --> pdb=" O HIS C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 998 removed outlier: 4.224A pdb=" N SER C 992 " --> pdb=" O ARG C 988 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR C 997 " --> pdb=" O ARG C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1012 removed outlier: 4.356A pdb=" N LEU C1008 " --> pdb=" O SER C1004 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C1009 " --> pdb=" O VAL C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1026 removed outlier: 3.726A pdb=" N ALA C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1117 Processing helix chain 'C' and resid 1124 through 1136 removed outlier: 3.644A pdb=" N ASP C1128 " --> pdb=" O HIS C1124 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1153 Processing helix chain 'C' and resid 1206 through 1216 removed outlier: 3.781A pdb=" N LYS C1212 " --> pdb=" O GLU C1208 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C1214 " --> pdb=" O ALA C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1235 Processing helix chain 'C' and resid 1238 through 1245 Processing helix chain 'C' and resid 1245 through 1252 removed outlier: 4.274A pdb=" N ARG C1251 " --> pdb=" O ARG C1247 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C1252 " --> pdb=" O HIS C1248 " (cutoff:3.500A) Processing helix chain 'C' and resid 1262 through 1267 removed outlier: 3.659A pdb=" N PHE C1266 " --> pdb=" O CYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1267 through 1275 removed outlier: 3.633A pdb=" N ALA C1273 " --> pdb=" O GLU C1269 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C1275 " --> pdb=" O ILE C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1288 removed outlier: 3.835A pdb=" N LEU C1286 " --> pdb=" O ILE C1282 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C1287 " --> pdb=" O ASP C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1313 through 1319 removed outlier: 3.999A pdb=" N LEU C1317 " --> pdb=" O ASN C1313 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR C1318 " --> pdb=" O PRO C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1329 through 1339 removed outlier: 3.502A pdb=" N MET C1333 " --> pdb=" O THR C1329 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C1336 " --> pdb=" O LEU C1332 " (cutoff:3.500A) Processing helix chain 'C' and resid 1340 through 1345 removed outlier: 4.357A pdb=" N PHE C1344 " --> pdb=" O ALA C1341 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C1345 " --> pdb=" O GLY C1342 " (cutoff:3.500A) Processing helix chain 'C' and resid 1361 through 1369 removed outlier: 4.694A pdb=" N LEU C1367 " --> pdb=" O GLN C1363 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 22 removed outlier: 3.683A pdb=" N HIS 5 22 " --> pdb=" O ASN 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 23 through 26 Processing helix chain '5' and resid 34 through 40 removed outlier: 3.694A pdb=" N LEU 5 38 " --> pdb=" O HIS 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 70 Processing helix chain '5' and resid 73 through 94 removed outlier: 3.876A pdb=" N GLU 5 79 " --> pdb=" O SER 5 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL 5 85 " --> pdb=" O GLU 5 81 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA 5 88 " --> pdb=" O CYS 5 84 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 5 89 " --> pdb=" O VAL 5 85 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR 5 93 " --> pdb=" O ARG 5 89 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR 5 94 " --> pdb=" O ARG 5 90 " (cutoff:3.500A) Processing helix chain '5' and resid 100 through 111 removed outlier: 3.794A pdb=" N ASP 5 104 " --> pdb=" O GLY 5 100 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 117 through 119 No H-bonds generated for 'chain '5' and resid 117 through 119' Processing helix chain '5' and resid 120 through 140 removed outlier: 3.541A pdb=" N SER 5 131 " --> pdb=" O ARG 5 127 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE 5 134 " --> pdb=" O VAL 5 130 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU 5 135 " --> pdb=" O SER 5 131 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS 5 137 " --> pdb=" O VAL 5 133 " (cutoff:3.500A) Processing helix chain '5' and resid 160 through 177 Processing helix chain '5' and resid 194 through 242 removed outlier: 3.628A pdb=" N ALA 5 199 " --> pdb=" O ALA 5 195 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR 5 206 " --> pdb=" O LYS 5 202 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA 5 226 " --> pdb=" O ARG 5 222 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN 5 229 " --> pdb=" O LEU 5 225 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS 5 237 " --> pdb=" O LYS 5 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET 5 241 " --> pdb=" O LYS 5 237 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS 5 242 " --> pdb=" O GLU 5 238 " (cutoff:3.500A) Processing helix chain '5' and resid 244 through 255 removed outlier: 3.616A pdb=" N ARG 5 251 " --> pdb=" O SER 5 247 " (cutoff:3.500A) Processing helix chain '5' and resid 260 through 274 removed outlier: 3.842A pdb=" N ALA 5 264 " --> pdb=" O ASN 5 260 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU 5 268 " --> pdb=" O ALA 5 264 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU 5 273 " --> pdb=" O GLU 5 269 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 279 removed outlier: 3.931A pdb=" N TYR 5 278 " --> pdb=" O ASP 5 274 " (cutoff:3.500A) Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '6' and resid 9 through 22 Processing helix chain '6' and resid 30 through 33 Processing helix chain '6' and resid 34 through 40 Processing helix chain '6' and resid 47 through 70 Processing helix chain '6' and resid 73 through 93 removed outlier: 3.611A pdb=" N GLU 6 81 " --> pdb=" O LEU 6 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA 6 86 " --> pdb=" O VAL 6 82 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL 6 87 " --> pdb=" O ARG 6 83 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA 6 88 " --> pdb=" O CYS 6 84 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG 6 89 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR 6 93 " --> pdb=" O ARG 6 89 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 111 removed outlier: 3.528A pdb=" N ALA 6 102 " --> pdb=" O ASP 6 98 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS 6 105 " --> pdb=" O LYS 6 101 " (cutoff:3.500A) Processing helix chain '6' and resid 120 through 141 removed outlier: 3.873A pdb=" N ILE 6 124 " --> pdb=" O HIS 6 120 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL 6 125 " --> pdb=" O ASP 6 121 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 177 removed outlier: 3.529A pdb=" N ASN 6 170 " --> pdb=" O ARG 6 166 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG 6 175 " --> pdb=" O LEU 6 171 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN 6 177 " --> pdb=" O GLY 6 173 " (cutoff:3.500A) Processing helix chain '6' and resid 194 through 241 removed outlier: 3.631A pdb=" N LEU 6 225 " --> pdb=" O GLU 6 221 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU 6 234 " --> pdb=" O GLU 6 230 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 6 237 " --> pdb=" O LYS 6 233 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET 6 241 " --> pdb=" O LYS 6 237 " (cutoff:3.500A) Processing helix chain '6' and resid 246 through 255 removed outlier: 3.511A pdb=" N ARG 6 251 " --> pdb=" O SER 6 247 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN 6 252 " --> pdb=" O ASN 6 248 " (cutoff:3.500A) Processing helix chain '6' and resid 261 through 274 Processing helix chain '6' and resid 274 through 279 removed outlier: 4.244A pdb=" N TYR 6 278 " --> pdb=" O ASP 6 274 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 282 No H-bonds generated for 'chain '6' and resid 280 through 282' Processing helix chain '4' and resid 9 through 22 removed outlier: 3.748A pdb=" N LEU 4 20 " --> pdb=" O LEU 4 16 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG 4 21 " --> pdb=" O VAL 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 40 removed outlier: 3.945A pdb=" N LEU 4 38 " --> pdb=" O HIS 4 34 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 69 Processing helix chain '4' and resid 73 through 92 removed outlier: 3.748A pdb=" N GLU 4 79 " --> pdb=" O SER 4 75 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU 4 81 " --> pdb=" O LEU 4 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG 4 90 " --> pdb=" O ALA 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 98 through 112 removed outlier: 4.035A pdb=" N ALA 4 102 " --> pdb=" O ASP 4 98 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP 4 104 " --> pdb=" O GLY 4 100 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS 4 105 " --> pdb=" O LYS 4 101 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR 4 112 " --> pdb=" O VAL 4 108 " (cutoff:3.500A) Processing helix chain '4' and resid 120 through 140 removed outlier: 4.016A pdb=" N GLU 4 126 " --> pdb=" O ALA 4 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL 4 130 " --> pdb=" O GLU 4 126 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER 4 131 " --> pdb=" O ARG 4 127 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET 4 138 " --> pdb=" O ILE 4 134 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL 4 140 " --> pdb=" O ALA 4 136 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 177 Processing helix chain '4' and resid 194 through 240 removed outlier: 4.165A pdb=" N ALA 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS 4 202 " --> pdb=" O ASN 4 198 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA 4 226 " --> pdb=" O ARG 4 222 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG 4 240 " --> pdb=" O VAL 4 236 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 255 removed outlier: 4.009A pdb=" N CYS 4 250 " --> pdb=" O ASP 4 246 " (cutoff:3.500A) Processing helix chain '4' and resid 260 through 274 removed outlier: 4.088A pdb=" N ALA 4 264 " --> pdb=" O ASN 4 260 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP 4 265 " --> pdb=" O GLY 4 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU 4 269 " --> pdb=" O ASP 4 265 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP 4 274 " --> pdb=" O LEU 4 270 " (cutoff:3.500A) Processing helix chain '4' and resid 274 through 279 removed outlier: 3.871A pdb=" N TYR 4 278 " --> pdb=" O ASP 4 274 " (cutoff:3.500A) Processing helix chain 'Z' and resid 14 through 24 Processing helix chain 'Z' and resid 37 through 49 removed outlier: 3.800A pdb=" N MET Z 43 " --> pdb=" O VAL Z 39 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS Z 46 " --> pdb=" O THR Z 42 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG Z 49 " --> pdb=" O SER Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 72 removed outlier: 4.261A pdb=" N PHE Z 60 " --> pdb=" O ASP Z 56 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS Z 61 " --> pdb=" O LYS Z 57 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Z 62 " --> pdb=" O CYS Z 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.646A pdb=" N MET D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 72 removed outlier: 3.728A pdb=" N LYS D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 24 Processing helix chain 'E' and resid 37 through 50 removed outlier: 4.844A pdb=" N SER E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 72 removed outlier: 4.278A pdb=" N PHE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 62 " --> pdb=" O CYS E 58 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 Processing helix chain 'p' and resid 18 through 28 removed outlier: 3.573A pdb=" N ALA p 26 " --> pdb=" O THR p 22 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 57 removed outlier: 3.748A pdb=" N VAL p 57 " --> pdb=" O GLU p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 84 through 89 removed outlier: 4.035A pdb=" N ILE p 89 " --> pdb=" O TYR p 85 " (cutoff:3.500A) Processing helix chain 'p' and resid 95 through 106 removed outlier: 3.747A pdb=" N SER p 104 " --> pdb=" O CYS p 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL p 105 " --> pdb=" O LEU p 101 " (cutoff:3.500A) Processing helix chain 'p' and resid 108 through 121 removed outlier: 3.809A pdb=" N ALA p 114 " --> pdb=" O ALA p 110 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY p 121 " --> pdb=" O TRP p 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 124 through 128 removed outlier: 4.169A pdb=" N ARG p 128 " --> pdb=" O LEU p 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 124 through 128' Processing helix chain 'p' and resid 156 through 160 removed outlier: 3.810A pdb=" N THR p 160 " --> pdb=" O THR p 157 " (cutoff:3.500A) Processing helix chain 'p' and resid 211 through 223 removed outlier: 3.776A pdb=" N GLY p 221 " --> pdb=" O ASP p 217 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS p 222 " --> pdb=" O VAL p 218 " (cutoff:3.500A) Processing helix chain 'p' and resid 223 through 237 Processing helix chain 'q' and resid 20 through 26 Processing helix chain 'q' and resid 48 through 52 Processing helix chain 'q' and resid 57 through 68 removed outlier: 3.817A pdb=" N LEU q 61 " --> pdb=" O GLY q 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG q 66 " --> pdb=" O ARG q 62 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN q 67 " --> pdb=" O GLY q 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET q 68 " --> pdb=" O LEU q 64 " (cutoff:3.500A) Processing helix chain 'q' and resid 140 through 158 removed outlier: 3.668A pdb=" N ASN q 147 " --> pdb=" O ALA q 143 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU q 158 " --> pdb=" O GLY q 154 " (cutoff:3.500A) Processing helix chain 'q' and resid 161 through 173 removed outlier: 3.508A pdb=" N ALA q 167 " --> pdb=" O GLU q 163 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN q 171 " --> pdb=" O ALA q 167 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN q 173 " --> pdb=" O VAL q 169 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 180 Processing helix chain 'q' and resid 190 through 209 removed outlier: 4.184A pdb=" N ASP q 196 " --> pdb=" O HIS q 192 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA q 208 " --> pdb=" O MET q 204 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN q 209 " --> pdb=" O SER q 205 " (cutoff:3.500A) Processing helix chain 'q' and resid 212 through 224 removed outlier: 3.504A pdb=" N THR q 217 " --> pdb=" O GLU q 213 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL q 219 " --> pdb=" O THR q 215 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG q 220 " --> pdb=" O MET q 216 " (cutoff:3.500A) Processing helix chain 'q' and resid 228 through 238 removed outlier: 3.804A pdb=" N LYS q 233 " --> pdb=" O MET q 229 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS q 234 " --> pdb=" O LEU q 230 " (cutoff:3.500A) Processing helix chain 'r' and resid 17 through 25 removed outlier: 3.507A pdb=" N GLY r 22 " --> pdb=" O ILE r 18 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS r 23 " --> pdb=" O ALA r 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU r 24 " --> pdb=" O ASP r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 52 Processing helix chain 'r' and resid 57 through 66 removed outlier: 3.633A pdb=" N LEU r 61 " --> pdb=" O GLY r 57 " (cutoff:3.500A) Processing helix chain 'r' and resid 140 through 157 removed outlier: 3.583A pdb=" N GLN r 148 " --> pdb=" O LEU r 144 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU r 151 " --> pdb=" O ASN r 147 " (cutoff:3.500A) Processing helix chain 'r' and resid 162 through 174 removed outlier: 3.786A pdb=" N GLN r 170 " --> pdb=" O LYS r 166 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR r 174 " --> pdb=" O GLN r 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 194 through 215 removed outlier: 3.787A pdb=" N ALA r 211 " --> pdb=" O VAL r 207 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER r 212 " --> pdb=" O ALA r 208 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU r 213 " --> pdb=" O ASN r 209 " (cutoff:3.500A) Processing helix chain 'r' and resid 215 through 223 removed outlier: 4.405A pdb=" N LYS r 221 " --> pdb=" O THR r 217 " (cutoff:3.500A) Processing helix chain 'r' and resid 230 through 238 removed outlier: 3.714A pdb=" N GLU r 236 " --> pdb=" O VAL r 232 " (cutoff:3.500A) Processing helix chain 'r' and resid 262 through 283 removed outlier: 3.589A pdb=" N ALA r 266 " --> pdb=" O ASP r 262 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU r 275 " --> pdb=" O LEU r 271 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG r 276 " --> pdb=" O PHE r 272 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP r 280 " --> pdb=" O ARG r 276 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU r 281 " --> pdb=" O GLN r 277 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG r 283 " --> pdb=" O ASP r 279 " (cutoff:3.500A) Processing helix chain 'r' and resid 295 through 297 No H-bonds generated for 'chain 'r' and resid 295 through 297' Processing sheet with id=AA1, first strand: chain 'J' and resid 34 through 38 removed outlier: 4.197A pdb=" N ALA J 34 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 91 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 303 through 304 removed outlier: 6.358A pdb=" N ILE J 78 " --> pdb=" O ILE J1059 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 90 through 96 Processing sheet with id=AA4, first strand: chain 'J' and resid 128 through 132 Processing sheet with id=AA5, first strand: chain 'J' and resid 262 through 263 removed outlier: 4.242A pdb=" N THR J 262 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 12.469A pdb=" N SER J 356 " --> pdb=" O ASN J 371 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N ASN J 371 " --> pdb=" O SER J 356 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP J 358 " --> pdb=" O MET J 369 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N MET J 273 " --> pdb=" O GLU J 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 262 through 263 removed outlier: 4.242A pdb=" N THR J 262 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 12.469A pdb=" N SER J 356 " --> pdb=" O ASN J 371 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N ASN J 371 " --> pdb=" O SER J 356 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP J 358 " --> pdb=" O MET J 369 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N MET J 273 " --> pdb=" O GLU J 370 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR J1041 " --> pdb=" O VAL J1102 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL J1102 " --> pdb=" O THR J1041 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU J1043 " --> pdb=" O ASN J1100 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU J1047 " --> pdb=" O VAL J1096 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL J1096 " --> pdb=" O LEU J1047 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR J1049 " --> pdb=" O THR J1094 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR J1094 " --> pdb=" O TYR J1049 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 428 through 431 Processing sheet with id=AA8, first strand: chain 'J' and resid 537 through 538 Processing sheet with id=AA9, first strand: chain 'J' and resid 697 through 698 Processing sheet with id=AB1, first strand: chain 'J' and resid 719 through 720 removed outlier: 3.511A pdb=" N GLU J 894 " --> pdb=" O VAL J 733 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 921 through 923 Processing sheet with id=AB3, first strand: chain 'J' and resid 1033 through 1034 Processing sheet with id=AB4, first strand: chain 'J' and resid 1326 through 1327 Processing sheet with id=AB5, first strand: chain 'A' and resid 34 through 38 removed outlier: 4.277A pdb=" N ALA A 34 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 38 " --> pdb=" O THR C 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 303 through 304 removed outlier: 6.297A pdb=" N ILE A 78 " --> pdb=" O ILE A1059 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 128 through 132 removed outlier: 3.528A pdb=" N LEU A 131 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A1064 " --> pdb=" O TYR p 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 292 through 298 removed outlier: 12.407A pdb=" N SER A 356 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N ASN A 371 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP A 358 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 275 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 292 through 298 removed outlier: 12.407A pdb=" N SER A 356 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N ASN A 371 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP A 358 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 275 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR A1041 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL A1102 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU A1043 " --> pdb=" O ASN A1100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A1098 " --> pdb=" O ASP A1045 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A1047 " --> pdb=" O VAL A1096 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL A1096 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR A1049 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR A1094 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 428 through 431 Processing sheet with id=AC2, first strand: chain 'A' and resid 537 through 538 Processing sheet with id=AC3, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AC4, first strand: chain 'A' and resid 719 through 720 removed outlier: 3.513A pdb=" N VAL A 720 " --> pdb=" O LEU A 917 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AC6, first strand: chain 'A' and resid 1033 through 1034 Processing sheet with id=AC7, first strand: chain 'A' and resid 1348 through 1350 removed outlier: 3.594A pdb=" N GLU A1348 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 303 through 304 removed outlier: 6.144A pdb=" N ILE C 78 " --> pdb=" O ILE C1059 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.832A pdb=" N ILE C 127 " --> pdb=" O VAL C1077 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 292 through 299 removed outlier: 12.434A pdb=" N SER C 356 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N ASN C 371 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP C 358 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 275 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR C1041 " --> pdb=" O VAL C1102 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL C1102 " --> pdb=" O THR C1041 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLU C1043 " --> pdb=" O ASN C1100 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C1098 " --> pdb=" O ASP C1045 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C1047 " --> pdb=" O VAL C1096 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL C1096 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR C1049 " --> pdb=" O THR C1094 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N THR C1094 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 292 through 299 removed outlier: 12.434A pdb=" N SER C 356 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N ASN C 371 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP C 358 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 275 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N LEU C1322 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 392 " --> pdb=" O LEU C1322 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 428 through 431 Processing sheet with id=AD4, first strand: chain 'C' and resid 537 through 538 Processing sheet with id=AD5, first strand: chain 'C' and resid 697 through 698 Processing sheet with id=AD6, first strand: chain 'C' and resid 719 through 720 Processing sheet with id=AD7, first strand: chain 'C' and resid 921 through 923 removed outlier: 3.516A pdb=" N CYS C 921 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1033 through 1034 Processing sheet with id=AD9, first strand: chain 'C' and resid 1326 through 1327 removed outlier: 3.624A pdb=" N SER C1326 " --> pdb=" O VAL C1356 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'p' and resid 46 through 51 removed outlier: 6.552A pdb=" N LEU p 46 " --> pdb=" O MET p 150 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU p 282 " --> pdb=" O LEU p 251 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU p 251 " --> pdb=" O GLU p 282 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL p 185 " --> pdb=" O LEU p 251 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TRP p 253 " --> pdb=" O GLN p 183 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN p 183 " --> pdb=" O TRP p 253 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR p 186 " --> pdb=" O LEU p 205 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG p 199 " --> pdb=" O ASP p 192 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR p 206 " --> pdb=" O LEU p 173 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'p' and resid 81 through 83 removed outlier: 5.952A pdb=" N LEU p 67 " --> pdb=" O LEU p 132 " (cutoff:3.500A) removed outlier: 20.266A pdb=" N GLU p 130 " --> pdb=" O TYR p 153 " (cutoff:3.500A) removed outlier: 17.886A pdb=" N TYR p 153 " --> pdb=" O GLU p 130 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU p 132 " --> pdb=" O ARG p 151 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG p 151 " --> pdb=" O LEU p 132 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS p 134 " --> pdb=" O VAL p 149 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU p 282 " --> pdb=" O LEU p 251 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU p 251 " --> pdb=" O GLU p 282 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY p 246 " --> pdb=" O PHE p 289 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE p 289 " --> pdb=" O GLY p 246 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'p' and resid 165 through 168 removed outlier: 3.696A pdb=" N HIS p 266 " --> pdb=" O LEU p 269 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'q' and resid 40 through 42 removed outlier: 7.910A pdb=" N ILE q 41 " --> pdb=" O ASN q 7 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE q 9 " --> pdb=" O ILE q 41 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'q' and resid 31 through 34 Processing sheet with id=AE6, first strand: chain 'q' and resid 108 through 111 Processing sheet with id=AE7, first strand: chain 'q' and resid 174 through 175 Processing sheet with id=AE8, first strand: chain 'r' and resid 9 through 11 Processing sheet with id=AE9, first strand: chain 'r' and resid 72 through 76 removed outlier: 6.651A pdb=" N LEU r 82 " --> pdb=" O ARG r 74 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'r' and resid 91 through 95 removed outlier: 7.095A pdb=" N SER r 299 " --> pdb=" O VAL r 293 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL r 293 " --> pdb=" O SER r 299 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR r 301 " --> pdb=" O CYS r 291 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE r 288 " --> pdb=" O LEU r 108 " (cutoff:3.500A) 1809 hydrogen bonds defined for protein. 5097 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: 20.06 Time building geometry restraints manager: 19.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9881 1.33 - 1.45: 10707 1.45 - 1.57: 27063 1.57 - 1.69: 1 1.69 - 1.81: 440 Bond restraints: 48092 Sorted by residual: bond pdb=" CA LEU J1287 " pdb=" C LEU J1287 " ideal model delta sigma weight residual 1.523 1.483 0.040 8.40e-03 1.42e+04 2.28e+01 bond pdb=" CA PRO C 717 " pdb=" C PRO C 717 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.21e+01 bond pdb=" CA LEU C1287 " pdb=" C LEU C1287 " ideal model delta sigma weight residual 1.523 1.495 0.028 8.40e-03 1.42e+04 1.12e+01 bond pdb=" CA LEU A1287 " pdb=" C LEU A1287 " ideal model delta sigma weight residual 1.523 1.497 0.026 8.40e-03 1.42e+04 9.84e+00 bond pdb=" C LEU A1176 " pdb=" N THR A1177 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 8.95e+00 ... (remaining 48087 not shown) Histogram of bond angle deviations from ideal: 96.42 - 103.97: 870 103.97 - 111.52: 22077 111.52 - 119.06: 17279 119.06 - 126.61: 24491 126.61 - 134.16: 657 Bond angle restraints: 65374 Sorted by residual: angle pdb=" C GLU J1138 " pdb=" N ARG J1139 " pdb=" CA ARG J1139 " ideal model delta sigma weight residual 123.10 128.31 -5.21 9.60e-01 1.09e+00 2.94e+01 angle pdb=" C VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta sigma weight residual 111.30 106.48 4.82 9.60e-01 1.09e+00 2.52e+01 angle pdb=" C ARG A 555 " pdb=" N ILE A 556 " pdb=" CA ILE A 556 " ideal model delta sigma weight residual 122.97 118.21 4.76 9.80e-01 1.04e+00 2.36e+01 angle pdb=" N LEU C 20 " pdb=" CA LEU C 20 " pdb=" C LEU C 20 " ideal model delta sigma weight residual 110.35 103.76 6.59 1.36e+00 5.41e-01 2.35e+01 angle pdb=" N VAL C 410 " pdb=" CA VAL C 410 " pdb=" C VAL C 410 " ideal model delta sigma weight residual 109.34 119.37 -10.03 2.08e+00 2.31e-01 2.32e+01 ... (remaining 65369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 26537 17.83 - 35.67: 2122 35.67 - 53.50: 410 53.50 - 71.33: 69 71.33 - 89.17: 16 Dihedral angle restraints: 29154 sinusoidal: 11745 harmonic: 17409 Sorted by residual: dihedral pdb=" CA ALA A 699 " pdb=" C ALA A 699 " pdb=" N GLU A 700 " pdb=" CA GLU A 700 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA THR p 72 " pdb=" C THR p 72 " pdb=" N GLY p 73 " pdb=" CA GLY p 73 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA SER A 5 " pdb=" C SER A 5 " pdb=" N ALA A 6 " pdb=" CA ALA A 6 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 29151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5636 0.055 - 0.110: 1682 0.110 - 0.165: 225 0.165 - 0.220: 12 0.220 - 0.275: 8 Chirality restraints: 7563 Sorted by residual: chirality pdb=" CA THR C 21 " pdb=" N THR C 21 " pdb=" C THR C 21 " pdb=" CB THR C 21 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB VAL J 23 " pdb=" CA VAL J 23 " pdb=" CG1 VAL J 23 " pdb=" CG2 VAL J 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL A 23 " pdb=" CA VAL A 23 " pdb=" CG1 VAL A 23 " pdb=" CG2 VAL A 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 7560 not shown) Planarity restraints: 8405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 989 " 0.057 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO J 990 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO J 990 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 990 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 343 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C SER A 343 " 0.053 2.00e-02 2.50e+03 pdb=" O SER A 343 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 344 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER J 343 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C SER J 343 " -0.050 2.00e-02 2.50e+03 pdb=" O SER J 343 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU J 344 " 0.017 2.00e-02 2.50e+03 ... (remaining 8402 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 42 1.84 - 2.61: 778 2.61 - 3.37: 64053 3.37 - 4.14: 106952 4.14 - 4.90: 202349 Nonbonded interactions: 374174 Sorted by model distance: nonbonded pdb=" CE1 PHE J 19 " pdb=" CB LEU A1088 " model vdw 1.080 3.740 nonbonded pdb=" NH1 ARG C 913 " pdb=" NE2 HIS C 981 " model vdw 1.096 3.200 nonbonded pdb=" OE1 GLU A 33 " pdb=" CD2 TYR C 119 " model vdw 1.136 3.340 nonbonded pdb=" CE LYS J 598 " pdb=" ND2 ASN J1000 " model vdw 1.205 3.520 nonbonded pdb=" NH1 ARG C 913 " pdb=" CD2 HIS C 981 " model vdw 1.284 3.340 ... (remaining 374169 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 '4' selection = chain '5' selection = chain '6' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 1 through 1139 or resid 1160 through 1370)) selection = (chain 'J' and (resid 1 through 1139 or resid 1160 through 1370)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.710 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 118.160 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4854 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 : 0.009 0.080 48092 Z= 0.606 Angle : 0.950 10.483 65374 Z= 0.532 Chirality : 0.050 0.275 7563 Planarity : 0.006 0.085 8405 Dihedral : 13.492 89.166 17823 Min Nonbonded Distance : 1.080 Molprobity Statistics. All-atom Clashscore : 26.90 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.92 % Favored : 94.50 % Rotamer: Outliers : 2.97 % Allowed : 10.51 % Favored : 86.52 % Cbeta Deviations : 0.02 % 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: -3.03 (0.10), residues: 5871 helix: -2.50 (0.08), residues: 2316 sheet: -2.70 (0.17), residues: 708 loop : -1.20 (0.11), residues: 2847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C1130 HIS 0.012 0.002 HIS C 748 PHE 0.034 0.003 PHE A 19 TYR 0.019 0.003 TYR C1301 ARG 0.015 0.001 ARG r 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1582 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1428 time to evaluate : 5.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 357 MET cc_start: 0.3526 (mmm) cc_final: 0.3295 (mmm) REVERT: J 511 GLU cc_start: 0.5207 (mm-30) cc_final: 0.3736 (tt0) REVERT: J 549 VAL cc_start: 0.4151 (OUTLIER) cc_final: 0.3549 (t) REVERT: J 636 VAL cc_start: 0.3347 (OUTLIER) cc_final: 0.2879 (p) REVERT: J 741 PRO cc_start: 0.4310 (Cg_endo) cc_final: 0.3198 (Cg_endo) REVERT: J 744 ILE cc_start: 0.4855 (mt) cc_final: 0.4462 (mm) REVERT: J 937 VAL cc_start: 0.5060 (OUTLIER) cc_final: 0.3938 (t) REVERT: J 991 PHE cc_start: 0.5273 (m-80) cc_final: 0.4797 (m-80) REVERT: J 1019 SER cc_start: 0.3457 (t) cc_final: 0.1988 (t) REVERT: J 1126 GLU cc_start: 0.6509 (tp30) cc_final: 0.6046 (tm-30) REVERT: J 1176 LEU cc_start: 0.6150 (mt) cc_final: 0.5673 (mt) REVERT: J 1254 TYR cc_start: 0.6181 (p90) cc_final: 0.5305 (p90) REVERT: J 1279 PHE cc_start: 0.6872 (m-80) cc_final: 0.6600 (m-80) REVERT: A 12 LYS cc_start: 0.2831 (mtmm) cc_final: 0.2315 (ttpp) REVERT: A 157 MET cc_start: 0.7277 (ttm) cc_final: 0.6575 (tpp) REVERT: A 198 GLU cc_start: 0.6717 (tt0) cc_final: 0.5667 (pt0) REVERT: A 214 ASN cc_start: 0.2724 (m-40) cc_final: 0.2496 (m-40) REVERT: A 256 ASP cc_start: 0.6406 (m-30) cc_final: 0.5554 (p0) REVERT: A 321 ILE cc_start: 0.5468 (mm) cc_final: 0.4835 (mm) REVERT: A 328 TYR cc_start: 0.6060 (m-80) cc_final: 0.5055 (m-10) REVERT: A 370 GLU cc_start: 0.5485 (tp30) cc_final: 0.4982 (tp30) REVERT: A 375 VAL cc_start: 0.4101 (OUTLIER) cc_final: 0.3383 (m) REVERT: A 384 PRO cc_start: 0.7265 (Cg_endo) cc_final: 0.6762 (Cg_exo) REVERT: A 440 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.6095 (tp) REVERT: A 576 TRP cc_start: 0.4742 (m100) cc_final: 0.4289 (m100) REVERT: A 785 TYR cc_start: 0.5780 (m-80) cc_final: 0.5115 (m-80) REVERT: A 1037 VAL cc_start: 0.7116 (m) cc_final: 0.6745 (t) REVERT: A 1119 MET cc_start: 0.6838 (mmm) cc_final: 0.6579 (mtt) REVERT: A 1199 MET cc_start: 0.5960 (mmp) cc_final: 0.4324 (mmp) REVERT: C 3 ASN cc_start: 0.7170 (t0) cc_final: 0.6601 (t0) REVERT: C 13 VAL cc_start: 0.2605 (OUTLIER) cc_final: 0.1184 (t) REVERT: C 15 ILE cc_start: 0.4010 (tp) cc_final: 0.3702 (mt) REVERT: C 31 MET cc_start: 0.4622 (tpt) cc_final: 0.4225 (tpt) REVERT: C 51 GLU cc_start: 0.6355 (tt0) cc_final: 0.4713 (tp30) REVERT: C 81 HIS cc_start: 0.6861 (m-70) cc_final: 0.6446 (m90) REVERT: C 91 MET cc_start: 0.6686 (mtm) cc_final: 0.5282 (pmm) REVERT: C 393 PHE cc_start: 0.6732 (m-80) cc_final: 0.6524 (m-80) REVERT: C 461 LEU cc_start: 0.5779 (tp) cc_final: 0.5266 (tt) REVERT: C 571 HIS cc_start: 0.3324 (m-70) cc_final: 0.2732 (m90) REVERT: C 969 HIS cc_start: 0.6222 (m-70) cc_final: 0.5325 (m-70) REVERT: C 1045 ASP cc_start: 0.5996 (m-30) cc_final: 0.5684 (m-30) REVERT: C 1074 THR cc_start: 0.3320 (p) cc_final: 0.1724 (m) REVERT: C 1208 GLU cc_start: 0.6855 (tp30) cc_final: 0.6632 (mm-30) REVERT: C 1219 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6930 (tp30) REVERT: 5 1 MET cc_start: 0.3801 (ttt) cc_final: 0.3257 (ttt) REVERT: 5 66 LEU cc_start: 0.4532 (mt) cc_final: 0.4310 (mp) REVERT: 5 133 VAL cc_start: 0.6746 (t) cc_final: 0.6365 (p) REVERT: 5 194 THR cc_start: 0.5751 (m) cc_final: 0.5314 (p) REVERT: 6 70 ASN cc_start: 0.7201 (t0) cc_final: 0.6742 (t0) REVERT: 6 118 VAL cc_start: 0.5509 (m) cc_final: 0.5005 (t) REVERT: 6 135 LEU cc_start: 0.4712 (tp) cc_final: 0.4337 (tt) REVERT: 6 174 VAL cc_start: 0.4544 (t) cc_final: 0.3833 (t) REVERT: 6 202 LYS cc_start: 0.4996 (mttp) cc_final: 0.4688 (mtpp) REVERT: 6 217 TRP cc_start: 0.6405 (t-100) cc_final: 0.5775 (t-100) REVERT: 6 241 MET cc_start: 0.6501 (mmm) cc_final: 0.6137 (mmp) REVERT: 6 253 ILE cc_start: 0.8043 (mm) cc_final: 0.7683 (mm) REVERT: 6 262 ASP cc_start: 0.6242 (m-30) cc_final: 0.5873 (m-30) REVERT: 6 273 GLU cc_start: 0.6585 (tt0) cc_final: 0.6379 (tt0) REVERT: 6 284 GLN cc_start: 0.6376 (pt0) cc_final: 0.6122 (pp30) REVERT: 4 1 MET cc_start: -0.1174 (mmm) cc_final: -0.1870 (tmm) REVERT: 4 28 ASP cc_start: 0.6876 (m-30) cc_final: 0.6648 (m-30) REVERT: 4 80 PHE cc_start: 0.3873 (t80) cc_final: 0.3543 (t80) REVERT: 4 212 ASN cc_start: 0.2867 (t0) cc_final: 0.2506 (m110) REVERT: 4 218 GLU cc_start: 0.7017 (tp30) cc_final: 0.6806 (tm-30) REVERT: D 70 VAL cc_start: 0.6504 (t) cc_final: 0.6013 (t) REVERT: E 16 GLU cc_start: 0.5972 (mt-10) cc_final: 0.5403 (tm-30) REVERT: E 47 TYR cc_start: 0.4008 (m-10) cc_final: 0.3303 (m-80) REVERT: E 73 THR cc_start: 0.8744 (p) cc_final: 0.8477 (p) REVERT: p 58 GLU cc_start: 0.5431 (pm20) cc_final: 0.4775 (pm20) REVERT: p 86 LEU cc_start: 0.6529 (tt) cc_final: 0.6119 (tt) REVERT: p 120 LEU cc_start: 0.3540 (OUTLIER) cc_final: 0.3125 (tp) REVERT: p 166 MET cc_start: 0.4401 (mmt) cc_final: 0.4193 (mmp) REVERT: q 95 LEU cc_start: 0.7478 (tt) cc_final: 0.7071 (tt) REVERT: q 201 CYS cc_start: 0.5213 (m) cc_final: 0.4920 (m) REVERT: r 4 MET cc_start: 0.2820 (ptm) cc_final: 0.1840 (mmm) REVERT: r 65 LEU cc_start: 0.5908 (tp) cc_final: 0.5597 (tp) REVERT: r 95 LEU cc_start: 0.7196 (tp) cc_final: 0.6699 (tp) REVERT: r 130 TRP cc_start: 0.3888 (t60) cc_final: 0.3527 (t60) REVERT: r 140 MET cc_start: 0.6224 (tpt) cc_final: 0.5992 (tpt) REVERT: r 164 GLU cc_start: 0.6609 (mp0) cc_final: 0.6273 (tm-30) REVERT: r 184 ILE cc_start: 0.6668 (mm) cc_final: 0.6369 (mm) REVERT: r 288 PHE cc_start: 0.4778 (m-80) cc_final: 0.4427 (m-10) outliers start: 154 outliers final: 57 residues processed: 1542 average time/residue: 0.6284 time to fit residues: 1568.4761 Evaluate side-chains 1015 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 951 time to evaluate : 4.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 549 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 636 VAL Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 687 ILE Chi-restraints excluded: chain J residue 754 VAL Chi-restraints excluded: chain J residue 764 GLU Chi-restraints excluded: chain J residue 811 LEU Chi-restraints excluded: chain J residue 861 VAL Chi-restraints excluded: chain J residue 937 VAL Chi-restraints excluded: chain J residue 948 ILE Chi-restraints excluded: chain J residue 953 SER Chi-restraints excluded: chain J residue 1037 VAL Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1096 VAL Chi-restraints excluded: chain J residue 1179 VAL Chi-restraints excluded: chain J residue 1239 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1365 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1328 THR Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 4 residue 6 ILE Chi-restraints excluded: chain 4 residue 253 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain p residue 120 LEU Chi-restraints excluded: chain p residue 272 SER Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 158 LEU Chi-restraints excluded: chain r residue 226 ASP Chi-restraints excluded: chain r residue 303 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 493 optimal weight: 0.9980 chunk 443 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 299 optimal weight: 0.0970 chunk 236 optimal weight: 5.9990 chunk 458 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 278 optimal weight: 7.9990 chunk 341 optimal weight: 0.5980 chunk 531 optimal weight: 5.9990 overall best weight: 1.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 ASN J 211 GLN ** J 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 485 GLN J 649 HIS ** J 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN J 889 HIS J 901 HIS J 903 GLN J 914 GLN J 915 HIS ** J 981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 985 ASN J1000 ASN J1003 HIS J1023 GLN J1029 HIS J1111 GLN ** J1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1353 ASN ** J1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 HIS ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 HIS A 713 HIS A 794 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN A1000 ASN A1133 HIS A1168 GLN ** A1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 205 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 304 ASN C 311 ASN C 485 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS C 737 GLN C 794 ASN C 849 GLN C 869 HIS C 889 HIS ** C 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN C 985 ASN C1000 ASN ** C1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1029 HIS C1061 ASN C1111 GLN C1168 GLN C1223 GLN C1350 HIS C1353 ASN ** C1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 54 ASN ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 105 HIS 5 229 GLN 5 252 ASN ** 6 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 170 ASN 6 256 HIS ** 4 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 252 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** p 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 249 GLN q 14 HIS ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 96 ASN ** q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 209 ASN r 50 GLN r 80 GLN r 171 GLN r 191 GLN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5173 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 48092 Z= 0.254 Angle : 0.741 13.490 65374 Z= 0.375 Chirality : 0.044 0.234 7563 Planarity : 0.005 0.067 8405 Dihedral : 6.440 72.565 6602 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.22 % Favored : 95.57 % Rotamer: Outliers : 3.47 % Allowed : 15.83 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.10), residues: 5871 helix: -1.10 (0.09), residues: 2379 sheet: -2.25 (0.19), residues: 642 loop : -0.85 (0.12), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP p 117 HIS 0.016 0.001 HIS 6 69 PHE 0.038 0.002 PHE C 942 TYR 0.018 0.002 TYR J1215 ARG 0.011 0.001 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1087 time to evaluate : 5.004 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: J 29 GLU cc_start: 0.6067 (mm-30) cc_final: 0.5692 (mm-30) REVERT: J 117 THR cc_start: 0.4835 (p) cc_final: 0.4264 (t) REVERT: J 199 ASN cc_start: 0.4437 (OUTLIER) cc_final: 0.4016 (p0) REVERT: J 357 MET cc_start: 0.4664 (mmm) cc_final: 0.4098 (mmm) REVERT: J 845 SER cc_start: 0.6529 (m) cc_final: 0.6069 (p) REVERT: J 1058 ILE cc_start: 0.6464 (mt) cc_final: 0.6167 (mt) REVERT: J 1138 GLU cc_start: 0.6669 (tt0) cc_final: 0.6378 (tp30) REVERT: J 1208 GLU cc_start: 0.5416 (tp30) cc_final: 0.5155 (tp30) REVERT: J 1254 TYR cc_start: 0.6559 (p90) cc_final: 0.5860 (p90) REVERT: J 1320 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6025 (mt-10) REVERT: A 12 LYS cc_start: 0.3078 (mtmm) cc_final: 0.2106 (ttmt) REVERT: A 32 PHE cc_start: 0.4317 (m-80) cc_final: 0.3687 (m-80) REVERT: A 93 PHE cc_start: 0.1249 (m-80) cc_final: 0.0849 (m-80) REVERT: A 157 MET cc_start: 0.7342 (ttm) cc_final: 0.6462 (tpp) REVERT: A 169 ASP cc_start: 0.7339 (t70) cc_final: 0.7125 (t70) REVERT: A 198 GLU cc_start: 0.6636 (tt0) cc_final: 0.5765 (pt0) REVERT: A 328 TYR cc_start: 0.5951 (m-80) cc_final: 0.5509 (m-80) REVERT: A 384 PRO cc_start: 0.7336 (Cg_endo) cc_final: 0.6780 (Cg_exo) REVERT: A 440 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.6011 (tp) REVERT: A 576 TRP cc_start: 0.5054 (m100) cc_final: 0.4590 (m100) REVERT: A 622 ASP cc_start: 0.6664 (t70) cc_final: 0.5925 (t0) REVERT: A 744 ILE cc_start: 0.6464 (mt) cc_final: 0.6142 (mp) REVERT: A 800 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4868 (pt) REVERT: A 1037 VAL cc_start: 0.6661 (m) cc_final: 0.6264 (t) REVERT: A 1038 ARG cc_start: 0.5801 (ttp-170) cc_final: 0.5450 (ptm160) REVERT: A 1111 GLN cc_start: 0.6496 (mt0) cc_final: 0.5904 (pm20) REVERT: A 1126 GLU cc_start: 0.6271 (tp30) cc_final: 0.5971 (tt0) REVERT: A 1188 ILE cc_start: 0.8015 (pt) cc_final: 0.7519 (pt) REVERT: A 1272 ILE cc_start: 0.6119 (mm) cc_final: 0.5489 (mt) REVERT: A 1308 GLU cc_start: 0.5906 (mp0) cc_final: 0.5688 (mp0) REVERT: A 1347 SER cc_start: 0.7894 (p) cc_final: 0.7360 (m) REVERT: C 3 ASN cc_start: 0.7197 (t0) cc_final: 0.6891 (t0) REVERT: C 51 GLU cc_start: 0.6367 (tt0) cc_final: 0.4748 (tp30) REVERT: C 331 HIS cc_start: 0.5700 (m-70) cc_final: 0.5416 (m90) REVERT: C 376 TYR cc_start: 0.6409 (m-80) cc_final: 0.6175 (m-10) REVERT: C 461 LEU cc_start: 0.5724 (tp) cc_final: 0.5396 (tt) REVERT: C 476 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7433 (mm110) REVERT: C 541 HIS cc_start: 0.6157 (OUTLIER) cc_final: 0.5670 (t-90) REVERT: C 625 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7489 (mp) REVERT: C 674 TYR cc_start: 0.5480 (m-80) cc_final: 0.4955 (m-80) REVERT: C 795 ASN cc_start: 0.7643 (t0) cc_final: 0.7029 (t0) REVERT: C 804 LEU cc_start: 0.7328 (mt) cc_final: 0.7074 (mt) REVERT: C 856 MET cc_start: 0.6904 (mtp) cc_final: 0.6623 (ttp) REVERT: C 905 GLN cc_start: 0.5864 (OUTLIER) cc_final: 0.4711 (tp40) REVERT: C 1006 MET cc_start: 0.4959 (mmt) cc_final: 0.4668 (mtm) REVERT: C 1156 MET cc_start: 0.4096 (mmm) cc_final: 0.3374 (mtm) REVERT: C 1212 LYS cc_start: 0.6285 (mptt) cc_final: 0.5767 (ttmt) REVERT: C 1288 ARG cc_start: 0.5348 (ptp-170) cc_final: 0.4949 (mtt-85) REVERT: C 1351 PHE cc_start: 0.5530 (OUTLIER) cc_final: 0.5135 (t80) REVERT: 5 25 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: 5 66 LEU cc_start: 0.4781 (mt) cc_final: 0.4550 (mt) REVERT: 5 121 ASP cc_start: 0.6493 (t70) cc_final: 0.6250 (t0) REVERT: 5 137 LYS cc_start: 0.5610 (mmtm) cc_final: 0.5342 (mmmt) REVERT: 5 175 ARG cc_start: 0.5467 (mtm110) cc_final: 0.5061 (mtm110) REVERT: 6 78 GLU cc_start: 0.7152 (pt0) cc_final: 0.6824 (mt-10) REVERT: 6 79 GLU cc_start: 0.7436 (tp30) cc_final: 0.6327 (tt0) REVERT: 6 105 HIS cc_start: 0.6931 (m-70) cc_final: 0.6720 (m-70) REVERT: 6 118 VAL cc_start: 0.5638 (m) cc_final: 0.5042 (t) REVERT: 6 196 LEU cc_start: 0.6008 (tt) cc_final: 0.5526 (tp) REVERT: 6 241 MET cc_start: 0.6415 (mmm) cc_final: 0.6144 (mmp) REVERT: 6 249 TYR cc_start: 0.4021 (t80) cc_final: 0.3806 (t80) REVERT: 6 278 TYR cc_start: 0.7738 (p90) cc_final: 0.7341 (p90) REVERT: 4 30 ASP cc_start: 0.7653 (t0) cc_final: 0.7414 (t0) REVERT: 4 165 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7966 (mt0) REVERT: 4 178 MET cc_start: 0.2498 (mpp) cc_final: 0.2195 (mpp) REVERT: 4 218 GLU cc_start: 0.7233 (tp30) cc_final: 0.6999 (tm-30) REVERT: Z 43 MET cc_start: 0.3836 (mmp) cc_final: 0.1914 (tpp) REVERT: D 17 LYS cc_start: 0.6748 (mtmm) cc_final: 0.6403 (ptpp) REVERT: D 19 ARG cc_start: 0.6720 (mmp80) cc_final: 0.6172 (mmm160) REVERT: E 16 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5854 (tm-30) REVERT: E 73 THR cc_start: 0.8823 (p) cc_final: 0.8482 (p) REVERT: p 49 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6803 (ttp80) REVERT: p 58 GLU cc_start: 0.6395 (pm20) cc_final: 0.5986 (mp0) REVERT: p 166 MET cc_start: 0.5292 (mmt) cc_final: 0.5058 (mmt) REVERT: q 95 LEU cc_start: 0.7236 (tt) cc_final: 0.6930 (tt) REVERT: q 130 TRP cc_start: 0.4592 (t60) cc_final: 0.4294 (t60) REVERT: r 4 MET cc_start: 0.3071 (ptm) cc_final: 0.1800 (mmm) REVERT: r 92 TYR cc_start: 0.5899 (m-80) cc_final: 0.5589 (m-80) REVERT: r 95 LEU cc_start: 0.7142 (tp) cc_final: 0.6831 (tp) REVERT: r 164 GLU cc_start: 0.6812 (mp0) cc_final: 0.6423 (tm-30) outliers start: 180 outliers final: 82 residues processed: 1203 average time/residue: 0.5689 time to fit residues: 1138.5137 Evaluate side-chains 980 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 890 time to evaluate : 5.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain J residue 484 GLN Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 687 ILE Chi-restraints excluded: chain J residue 764 GLU Chi-restraints excluded: chain J residue 922 CYS Chi-restraints excluded: chain J residue 937 VAL Chi-restraints excluded: chain J residue 1055 THR Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1063 ILE Chi-restraints excluded: chain J residue 1215 TYR Chi-restraints excluded: chain J residue 1239 LEU Chi-restraints excluded: chain J residue 1242 VAL Chi-restraints excluded: chain J residue 1256 SER Chi-restraints excluded: chain J residue 1287 LEU Chi-restraints excluded: chain J residue 1355 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 HIS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 541 HIS Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 905 GLN Chi-restraints excluded: chain C residue 915 HIS Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1064 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1121 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1324 ILE Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain 5 residue 25 GLN Chi-restraints excluded: chain 5 residue 151 THR Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 266 THR Chi-restraints excluded: chain 4 residue 2 SER Chi-restraints excluded: chain 4 residue 76 VAL Chi-restraints excluded: chain 4 residue 244 SER Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain p residue 47 THR Chi-restraints excluded: chain p residue 83 SER Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain p residue 173 LEU Chi-restraints excluded: chain p residue 261 THR Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 283 LEU Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 101 THR Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 182 PHE Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain r residue 11 THR Chi-restraints excluded: chain r residue 104 LYS Chi-restraints excluded: chain r residue 126 THR Chi-restraints excluded: chain r residue 174 THR Chi-restraints excluded: chain r residue 219 VAL Chi-restraints excluded: chain r residue 291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 295 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 442 optimal weight: 20.0000 chunk 361 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 532 optimal weight: 20.0000 chunk 574 optimal weight: 20.0000 chunk 473 optimal weight: 20.0000 chunk 527 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 ASN J 22 HIS J 84 ASN ** J 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 GLN ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 541 HIS J 571 HIS J 618 HIS J 713 HIS J 726 ASN J 794 ASN J1023 GLN ** J1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 HIS A 560 ASN A 711 HIS ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 HIS A1079 GLN A1111 GLN A1168 GLN ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 HIS C 311 ASN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 673 HIS ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 743 ASN C 903 GLN C 905 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS ** C1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN ** C1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 34 HIS ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 105 HIS 5 248 ASN ** 6 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 170 ASN ** 6 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 248 ASN 4 9 GLN ** 4 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 177 ASN 4 191 HIS D 20 HIS ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 249 GLN ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 HIS ** q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 45 GLN r 84 HIS r 171 GLN ** r 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.8924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.172 48092 Z= 0.519 Angle : 1.094 17.299 65374 Z= 0.560 Chirality : 0.059 0.620 7563 Planarity : 0.009 0.123 8405 Dihedral : 7.075 76.820 6532 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.90 % Rotamer: Outliers : 6.67 % Allowed : 17.37 % Favored : 75.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.10), residues: 5871 helix: -1.49 (0.09), residues: 2403 sheet: -2.03 (0.18), residues: 682 loop : -1.37 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.004 TRP p 117 HIS 0.034 0.003 HIS A1217 PHE 0.048 0.004 PHE A 19 TYR 0.056 0.004 TYR C 522 ARG 0.013 0.001 ARG p 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2017 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1671 time to evaluate : 4.793 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: J 31 MET cc_start: 0.8224 (mmt) cc_final: 0.7884 (tpp) REVERT: J 217 GLN cc_start: 0.7606 (tp40) cc_final: 0.6684 (mt0) REVERT: J 310 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5338 (mm-30) REVERT: J 318 TYR cc_start: 0.8433 (m-80) cc_final: 0.8110 (m-80) REVERT: J 387 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7172 (mmt90) REVERT: J 404 ASP cc_start: 0.7799 (m-30) cc_final: 0.6917 (t0) REVERT: J 439 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8074 (tttt) REVERT: J 442 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.5977 (t80) REVERT: J 459 PRO cc_start: 0.7074 (Cg_exo) cc_final: 0.6867 (Cg_endo) REVERT: J 493 ARG cc_start: 0.7720 (mmt180) cc_final: 0.6519 (mtm-85) REVERT: J 511 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6154 (mt-10) REVERT: J 760 MET cc_start: 0.5392 (mpp) cc_final: 0.4811 (mtt) REVERT: J 785 TYR cc_start: 0.8459 (m-10) cc_final: 0.8250 (m-10) REVERT: J 815 PRO cc_start: 0.8437 (Cg_exo) cc_final: 0.8116 (Cg_endo) REVERT: J 899 LEU cc_start: 0.6596 (mt) cc_final: 0.6351 (mp) REVERT: J 935 LEU cc_start: 0.7337 (mp) cc_final: 0.7124 (mt) REVERT: J 1080 ASN cc_start: 0.7759 (t0) cc_final: 0.7195 (t0) REVERT: J 1101 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6098 (ptt180) REVERT: J 1112 ASP cc_start: 0.5152 (p0) cc_final: 0.4683 (p0) REVERT: J 1120 ASN cc_start: 0.7654 (m110) cc_final: 0.7397 (m110) REVERT: J 1126 GLU cc_start: 0.8585 (tp30) cc_final: 0.8323 (mm-30) REVERT: J 1143 LEU cc_start: 0.7276 (mm) cc_final: 0.6803 (mt) REVERT: J 1183 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7437 (p) REVERT: J 1212 LYS cc_start: 0.8059 (mttt) cc_final: 0.7846 (ttmm) REVERT: J 1217 HIS cc_start: 0.6292 (m90) cc_final: 0.6035 (m90) REVERT: J 1334 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6235 (mt-10) REVERT: A 35 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6736 (pt) REVERT: A 58 CYS cc_start: 0.8047 (p) cc_final: 0.7201 (m) REVERT: A 65 TYR cc_start: 0.7527 (m-80) cc_final: 0.7225 (m-80) REVERT: A 149 ASP cc_start: 0.6144 (t70) cc_final: 0.5869 (m-30) REVERT: A 150 LYS cc_start: 0.7279 (mmtp) cc_final: 0.6467 (mtpt) REVERT: A 157 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6953 (tpp) REVERT: A 257 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7164 (p0) REVERT: A 329 LYS cc_start: 0.6982 (ttpp) cc_final: 0.6101 (tptm) REVERT: A 336 GLN cc_start: 0.7201 (mt0) cc_final: 0.6987 (tm-30) REVERT: A 357 MET cc_start: 0.7318 (tpt) cc_final: 0.7071 (tpp) REVERT: A 360 ILE cc_start: 0.8527 (tp) cc_final: 0.8056 (tt) REVERT: A 361 ARG cc_start: 0.7567 (ptp-170) cc_final: 0.7203 (mmm160) REVERT: A 373 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8048 (tpp-160) REVERT: A 405 ARG cc_start: 0.6831 (mtm-85) cc_final: 0.6510 (mmt-90) REVERT: A 440 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7890 (tt) REVERT: A 465 THR cc_start: 0.7608 (m) cc_final: 0.7242 (p) REVERT: A 475 MET cc_start: 0.6500 (mmt) cc_final: 0.6193 (mmt) REVERT: A 737 GLN cc_start: 0.8193 (tt0) cc_final: 0.7952 (pm20) REVERT: A 807 LEU cc_start: 0.6346 (tp) cc_final: 0.6122 (tp) REVERT: A 867 ASP cc_start: 0.7625 (t0) cc_final: 0.6702 (t0) REVERT: A 894 GLU cc_start: 0.6511 (tt0) cc_final: 0.5629 (tt0) REVERT: A 908 PRO cc_start: 0.8886 (Cg_endo) cc_final: 0.8603 (Cg_exo) REVERT: A 927 PRO cc_start: 0.7769 (Cg_exo) cc_final: 0.7376 (Cg_endo) REVERT: A 940 HIS cc_start: 0.7713 (t-90) cc_final: 0.7280 (t-170) REVERT: A 946 PRO cc_start: 0.8359 (Cg_exo) cc_final: 0.8141 (Cg_endo) REVERT: A 973 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6246 (p90) REVERT: A 983 TYR cc_start: 0.8337 (m-80) cc_final: 0.7831 (m-80) REVERT: A 1015 ILE cc_start: 0.7927 (mt) cc_final: 0.7281 (mt) REVERT: A 1021 VAL cc_start: 0.7218 (OUTLIER) cc_final: 0.6989 (t) REVERT: A 1041 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.7723 (p) REVERT: A 1125 ASP cc_start: 0.7996 (t0) cc_final: 0.7525 (t0) REVERT: A 1128 ASP cc_start: 0.6543 (t70) cc_final: 0.6336 (t0) REVERT: A 1280 LYS cc_start: 0.6579 (mmtm) cc_final: 0.6145 (tttt) REVERT: A 1297 THR cc_start: 0.7673 (p) cc_final: 0.7384 (p) REVERT: A 1308 GLU cc_start: 0.6478 (mp0) cc_final: 0.6089 (mp0) REVERT: A 1346 THR cc_start: 0.8277 (t) cc_final: 0.8069 (p) REVERT: C 9 LEU cc_start: 0.8081 (mp) cc_final: 0.7879 (mt) REVERT: C 29 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7341 (mm-30) REVERT: C 36 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7236 (mmm-85) REVERT: C 45 ARG cc_start: 0.6573 (ttp-170) cc_final: 0.6152 (ttp-110) REVERT: C 46 TYR cc_start: 0.5915 (m-80) cc_final: 0.5682 (m-80) REVERT: C 91 MET cc_start: 0.8086 (mtp) cc_final: 0.7819 (mtm) REVERT: C 186 LYS cc_start: 0.6695 (ttpt) cc_final: 0.6249 (tttm) REVERT: C 236 ARG cc_start: 0.6642 (ttt-90) cc_final: 0.6377 (ttp80) REVERT: C 292 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7791 (p) REVERT: C 360 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7361 (tt) REVERT: C 361 ARG cc_start: 0.7459 (mmt-90) cc_final: 0.7112 (mpt180) REVERT: C 369 MET cc_start: 0.7894 (mmt) cc_final: 0.7627 (ptt) REVERT: C 434 ASP cc_start: 0.8123 (p0) cc_final: 0.7896 (p0) REVERT: C 493 ARG cc_start: 0.8041 (tmm-80) cc_final: 0.7003 (mtm-85) REVERT: C 503 ARG cc_start: 0.7344 (mtp180) cc_final: 0.7050 (mtp180) REVERT: C 538 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6589 (p0) REVERT: C 577 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6865 (mt-10) REVERT: C 598 LYS cc_start: 0.7240 (ttpp) cc_final: 0.6803 (tptp) REVERT: C 642 ARG cc_start: 0.5959 (OUTLIER) cc_final: 0.4907 (mtt90) REVERT: C 727 MET cc_start: 0.4697 (ptp) cc_final: 0.4455 (mtp) REVERT: C 736 ARG cc_start: 0.6420 (mtm-85) cc_final: 0.5951 (mtp85) REVERT: C 771 TYR cc_start: 0.7332 (t80) cc_final: 0.7125 (t80) REVERT: C 802 LEU cc_start: 0.8809 (mt) cc_final: 0.8519 (tp) REVERT: C 804 LEU cc_start: 0.7740 (mt) cc_final: 0.7521 (mt) REVERT: C 909 ASP cc_start: 0.9045 (t70) cc_final: 0.8774 (p0) REVERT: C 912 SER cc_start: 0.8396 (m) cc_final: 0.8063 (p) REVERT: C 915 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.6884 (t-90) REVERT: C 945 ASN cc_start: 0.7647 (t0) cc_final: 0.7272 (t0) REVERT: C 968 ARG cc_start: 0.7068 (ptm-80) cc_final: 0.6530 (ptt180) REVERT: C 1037 VAL cc_start: 0.6749 (OUTLIER) cc_final: 0.6408 (m) REVERT: C 1058 ILE cc_start: 0.6147 (pt) cc_final: 0.5197 (pt) REVERT: C 1070 ASP cc_start: 0.7887 (t0) cc_final: 0.7484 (t70) REVERT: C 1113 LEU cc_start: 0.4878 (OUTLIER) cc_final: 0.4670 (tt) REVERT: C 1115 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6441 (mtt90) REVERT: C 1132 ARG cc_start: 0.6805 (mmt90) cc_final: 0.6513 (mmm-85) REVERT: C 1137 VAL cc_start: 0.7181 (OUTLIER) cc_final: 0.6774 (p) REVERT: C 1164 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.7987 (t) REVERT: C 1212 LYS cc_start: 0.6572 (mptt) cc_final: 0.6231 (ttmt) REVERT: C 1219 GLU cc_start: 0.8834 (tp30) cc_final: 0.8630 (tp30) REVERT: C 1244 TYR cc_start: 0.7904 (m-80) cc_final: 0.6606 (m-80) REVERT: C 1247 ARG cc_start: 0.8586 (ttt90) cc_final: 0.8240 (mtp180) REVERT: C 1271 ILE cc_start: 0.7766 (tp) cc_final: 0.7319 (pt) REVERT: C 1358 GLU cc_start: 0.5911 (pt0) cc_final: 0.5226 (pm20) REVERT: 5 25 GLN cc_start: 0.7758 (tt0) cc_final: 0.7041 (pt0) REVERT: 5 68 PHE cc_start: 0.5605 (t80) cc_final: 0.5177 (t80) REVERT: 5 135 LEU cc_start: 0.6813 (tp) cc_final: 0.6594 (mt) REVERT: 5 137 LYS cc_start: 0.6135 (mmtm) cc_final: 0.5539 (mmmt) REVERT: 5 196 LEU cc_start: 0.8032 (tt) cc_final: 0.7788 (tp) REVERT: 5 237 LYS cc_start: 0.6937 (mttt) cc_final: 0.6700 (mmtp) REVERT: 5 247 SER cc_start: 0.7380 (OUTLIER) cc_final: 0.7052 (m) REVERT: 5 263 SER cc_start: 0.7253 (OUTLIER) cc_final: 0.6922 (p) REVERT: 5 269 GLU cc_start: 0.3583 (mt-10) cc_final: 0.3297 (mt-10) REVERT: 6 51 VAL cc_start: 0.5334 (t) cc_final: 0.4795 (m) REVERT: 6 105 HIS cc_start: 0.7154 (m-70) cc_final: 0.6800 (m170) REVERT: 6 137 LYS cc_start: 0.6612 (mmtp) cc_final: 0.5962 (mttp) REVERT: 6 160 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6548 (mttp) REVERT: 6 163 GLU cc_start: 0.6358 (mm-30) cc_final: 0.6120 (mm-30) REVERT: 6 178 MET cc_start: 0.6357 (pmm) cc_final: 0.5355 (pmm) REVERT: 6 211 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6677 (mtt) REVERT: 6 237 LYS cc_start: 0.7166 (mttt) cc_final: 0.6705 (tptt) REVERT: 6 238 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7280 (mt-10) REVERT: 6 240 ARG cc_start: 0.6629 (ttp-110) cc_final: 0.6318 (ttp-110) REVERT: 6 241 MET cc_start: 0.6296 (mmm) cc_final: 0.6066 (mmp) REVERT: 6 266 THR cc_start: 0.8021 (m) cc_final: 0.7647 (p) REVERT: 6 269 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7712 (tp30) REVERT: 6 284 GLN cc_start: 0.7197 (pp30) cc_final: 0.6774 (pt0) REVERT: 4 1 MET cc_start: 0.0948 (tmm) cc_final: -0.0907 (mpp) REVERT: 4 6 ILE cc_start: 0.6565 (OUTLIER) cc_final: 0.6058 (mm) REVERT: 4 40 LYS cc_start: 0.5047 (mmtt) cc_final: 0.4833 (mmtm) REVERT: 4 62 TYR cc_start: 0.5490 (t80) cc_final: 0.4989 (t80) REVERT: 4 111 ARG cc_start: 0.6625 (mtp-110) cc_final: 0.6380 (ttp80) REVERT: 4 178 MET cc_start: 0.2932 (mpp) cc_final: 0.2555 (mpp) REVERT: 4 212 ASN cc_start: 0.5220 (m-40) cc_final: 0.4669 (m110) REVERT: 4 221 GLU cc_start: 0.6934 (tt0) cc_final: 0.6677 (mm-30) REVERT: 4 243 LEU cc_start: 0.6946 (mt) cc_final: 0.6603 (mp) REVERT: 4 280 ASP cc_start: 0.6879 (t0) cc_final: 0.6539 (m-30) REVERT: Z 42 THR cc_start: 0.6531 (p) cc_final: 0.6257 (p) REVERT: Z 72 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5656 (mtp85) REVERT: D 19 ARG cc_start: 0.7735 (mmp80) cc_final: 0.7345 (mtp180) REVERT: D 23 ASN cc_start: 0.7424 (m-40) cc_final: 0.7159 (m110) REVERT: D 27 GLU cc_start: 0.8412 (tt0) cc_final: 0.8208 (tt0) REVERT: D 61 LYS cc_start: 0.7126 (mtmt) cc_final: 0.6754 (mttm) REVERT: p 49 ARG cc_start: 0.7561 (ttm110) cc_final: 0.6853 (ttp80) REVERT: p 58 GLU cc_start: 0.7057 (pm20) cc_final: 0.6629 (mp0) REVERT: p 84 LEU cc_start: 0.8271 (tp) cc_final: 0.7862 (tp) REVERT: p 101 LEU cc_start: 0.7781 (tt) cc_final: 0.7573 (tt) REVERT: p 117 TRP cc_start: 0.5447 (m-10) cc_final: 0.4890 (m-10) REVERT: p 150 MET cc_start: 0.7080 (mmm) cc_final: 0.6721 (mmm) REVERT: p 153 TYR cc_start: 0.7568 (m-80) cc_final: 0.6492 (m-80) REVERT: p 166 MET cc_start: 0.7311 (mmt) cc_final: 0.7046 (mmm) REVERT: p 192 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.5966 (p0) REVERT: p 225 ARG cc_start: 0.8520 (tmm-80) cc_final: 0.8203 (tpm170) REVERT: q 140 MET cc_start: 0.7630 (tpp) cc_final: 0.7425 (tpt) REVERT: q 165 VAL cc_start: 0.7397 (t) cc_final: 0.7048 (m) REVERT: q 201 CYS cc_start: 0.6563 (t) cc_final: 0.6235 (t) REVERT: q 207 VAL cc_start: 0.7609 (t) cc_final: 0.7392 (t) REVERT: r 4 MET cc_start: 0.4696 (ptm) cc_final: 0.3845 (mmm) REVERT: r 26 LYS cc_start: 0.8811 (mptt) cc_final: 0.8499 (mmmt) REVERT: r 37 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6768 (mtm180) REVERT: r 48 LEU cc_start: 0.7442 (tt) cc_final: 0.7143 (tp) REVERT: r 140 MET cc_start: 0.7919 (tmm) cc_final: 0.7483 (tmm) REVERT: r 145 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6702 (tm-30) REVERT: r 163 GLU cc_start: 0.8648 (tt0) cc_final: 0.7652 (mp0) REVERT: r 164 GLU cc_start: 0.7931 (mp0) cc_final: 0.7485 (tm-30) REVERT: r 170 GLN cc_start: 0.7952 (mt0) cc_final: 0.7208 (mp10) REVERT: r 173 GLN cc_start: 0.8462 (mt0) cc_final: 0.8258 (mt0) REVERT: r 198 LYS cc_start: 0.7751 (tppt) cc_final: 0.7548 (ttpt) REVERT: r 216 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5850 (tpt) REVERT: r 225 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5187 (tm-30) REVERT: r 294 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7596 (p) outliers start: 346 outliers final: 122 residues processed: 1865 average time/residue: 0.6093 time to fit residues: 1874.1624 Evaluate side-chains 1458 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1304 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain J residue 439 LYS Chi-restraints excluded: chain J residue 442 PHE Chi-restraints excluded: chain J residue 481 CYS Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 698 LEU Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 764 GLU Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 802 LEU Chi-restraints excluded: chain J residue 892 VAL Chi-restraints excluded: chain J residue 942 PHE Chi-restraints excluded: chain J residue 947 THR Chi-restraints excluded: chain J residue 952 LEU Chi-restraints excluded: chain J residue 1000 ASN Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1048 LEU Chi-restraints excluded: chain J residue 1064 VAL Chi-restraints excluded: chain J residue 1071 ILE Chi-restraints excluded: chain J residue 1081 ILE Chi-restraints excluded: chain J residue 1085 ASP Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1181 MET Chi-restraints excluded: chain J residue 1183 VAL Chi-restraints excluded: chain J residue 1215 TYR Chi-restraints excluded: chain J residue 1242 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1215 TYR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 552 CYS Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 915 HIS Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1076 HIS Chi-restraints excluded: chain C residue 1083 THR Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1121 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1159 ARG Chi-restraints excluded: chain C residue 1164 THR Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1177 THR Chi-restraints excluded: chain C residue 1198 CYS Chi-restraints excluded: chain C residue 1234 SER Chi-restraints excluded: chain C residue 1355 VAL Chi-restraints excluded: chain C residue 1366 MET Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 93 THR Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain 5 residue 151 THR Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 247 SER Chi-restraints excluded: chain 5 residue 263 SER Chi-restraints excluded: chain 6 residue 37 ILE Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 98 ASP Chi-restraints excluded: chain 6 residue 160 LYS Chi-restraints excluded: chain 6 residue 191 HIS Chi-restraints excluded: chain 6 residue 211 MET Chi-restraints excluded: chain 6 residue 242 CYS Chi-restraints excluded: chain 6 residue 246 ASP Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 4 residue 6 ILE Chi-restraints excluded: chain 4 residue 12 ASP Chi-restraints excluded: chain 4 residue 20 LEU Chi-restraints excluded: chain 4 residue 76 VAL Chi-restraints excluded: chain 4 residue 206 THR Chi-restraints excluded: chain 4 residue 244 SER Chi-restraints excluded: chain 4 residue 255 LYS Chi-restraints excluded: chain Z residue 72 ARG Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain p residue 47 THR Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain p residue 104 SER Chi-restraints excluded: chain p residue 115 LEU Chi-restraints excluded: chain p residue 158 LEU Chi-restraints excluded: chain p residue 160 THR Chi-restraints excluded: chain p residue 173 LEU Chi-restraints excluded: chain p residue 192 ASP Chi-restraints excluded: chain p residue 245 THR Chi-restraints excluded: chain p residue 261 THR Chi-restraints excluded: chain p residue 283 LEU Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 101 THR Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain r residue 126 THR Chi-restraints excluded: chain r residue 148 GLN Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 216 MET Chi-restraints excluded: chain r residue 225 GLU Chi-restraints excluded: chain r residue 259 VAL Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain r residue 294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 525 optimal weight: 1.9990 chunk 400 optimal weight: 0.0970 chunk 276 optimal weight: 40.0000 chunk 58 optimal weight: 0.0770 chunk 253 optimal weight: 8.9990 chunk 357 optimal weight: 0.8980 chunk 534 optimal weight: 20.0000 chunk 565 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 506 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 177 HIS J 199 ASN ** J 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 620 ASN ** J 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 940 HIS J1003 HIS J1023 GLN J1264 GLN ** J1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN A 346 GLN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 HIS ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 HIS A1111 GLN A1133 HIS ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 884 GLN C 965 HIS ** C1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1223 GLN ** C1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 54 ASN ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 105 HIS 5 248 ASN ** 6 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 248 ASN 4 120 HIS ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 HIS D 37 HIS p 43 HIS ** p 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 7 ASN r 45 GLN r 80 GLN r 173 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.9441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 48092 Z= 0.201 Angle : 0.697 15.575 65374 Z= 0.345 Chirality : 0.043 0.308 7563 Planarity : 0.005 0.066 8405 Dihedral : 5.763 68.149 6518 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 4.36 % Allowed : 22.66 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 5871 helix: -0.63 (0.10), residues: 2429 sheet: -1.66 (0.19), residues: 633 loop : -1.13 (0.12), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP p 117 HIS 0.016 0.001 HIS A1029 PHE 0.024 0.002 PHE 4 19 TYR 0.023 0.002 TYR C 38 ARG 0.012 0.001 ARG 5 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1628 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1402 time to evaluate : 4.869 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: J 31 MET cc_start: 0.8212 (mmt) cc_final: 0.7985 (tpp) REVERT: J 140 ARG cc_start: 0.7095 (mtm180) cc_final: 0.6811 (mtm180) REVERT: J 217 GLN cc_start: 0.7610 (tp40) cc_final: 0.6770 (mt0) REVERT: J 237 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6768 (t70) REVERT: J 310 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5955 (mm-30) REVERT: J 318 TYR cc_start: 0.8438 (m-80) cc_final: 0.8057 (m-80) REVERT: J 388 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7837 (p0) REVERT: J 403 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7474 (mt-10) REVERT: J 439 LYS cc_start: 0.8374 (pttt) cc_final: 0.7788 (tttm) REVERT: J 442 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.6264 (t80) REVERT: J 513 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7519 (mtpt) REVERT: J 737 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7451 (tp40) REVERT: J 760 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5219 (mtt) REVERT: J 845 SER cc_start: 0.6434 (m) cc_final: 0.6219 (p) REVERT: J 911 ILE cc_start: 0.7872 (mt) cc_final: 0.7630 (mm) REVERT: J 1101 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5974 (ptt180) REVERT: J 1113 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7054 (mp) REVERT: J 1190 ASN cc_start: 0.8078 (t0) cc_final: 0.7532 (m110) REVERT: A 35 LEU cc_start: 0.6952 (pt) cc_final: 0.6619 (pt) REVERT: A 58 CYS cc_start: 0.8030 (p) cc_final: 0.7179 (m) REVERT: A 65 TYR cc_start: 0.7476 (m-80) cc_final: 0.7271 (m-80) REVERT: A 122 LYS cc_start: 0.8186 (mttp) cc_final: 0.7966 (mmtm) REVERT: A 149 ASP cc_start: 0.6725 (t70) cc_final: 0.6409 (m-30) REVERT: A 150 LYS cc_start: 0.7263 (mmtp) cc_final: 0.6398 (mtpt) REVERT: A 157 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6781 (tpp) REVERT: A 171 MET cc_start: 0.7713 (mmm) cc_final: 0.7504 (tpp) REVERT: A 232 ARG cc_start: 0.7097 (ttm170) cc_final: 0.5945 (mtt-85) REVERT: A 241 LYS cc_start: 0.7337 (ptmm) cc_final: 0.6949 (tttt) REVERT: A 245 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7635 (mtp85) REVERT: A 246 LEU cc_start: 0.7781 (tp) cc_final: 0.7461 (mt) REVERT: A 257 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7234 (p0) REVERT: A 295 THR cc_start: 0.6664 (p) cc_final: 0.6287 (p) REVERT: A 310 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6436 (mm-30) REVERT: A 329 LYS cc_start: 0.6952 (ttpp) cc_final: 0.6356 (tptt) REVERT: A 357 MET cc_start: 0.7711 (tpt) cc_final: 0.7438 (tpp) REVERT: A 360 ILE cc_start: 0.8404 (tp) cc_final: 0.8055 (tt) REVERT: A 374 ARG cc_start: 0.9014 (ptp90) cc_final: 0.8582 (ptp90) REVERT: A 405 ARG cc_start: 0.7021 (mtm-85) cc_final: 0.6547 (mmt-90) REVERT: A 416 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7864 (mt) REVERT: A 476 GLN cc_start: 0.7938 (mm110) cc_final: 0.7720 (mm110) REVERT: A 498 PHE cc_start: 0.8140 (t80) cc_final: 0.7900 (t80) REVERT: A 538 ASP cc_start: 0.6862 (t0) cc_final: 0.6467 (t0) REVERT: A 580 GLU cc_start: 0.7943 (tp30) cc_final: 0.7723 (tt0) REVERT: A 651 TYR cc_start: 0.7993 (t80) cc_final: 0.7686 (t80) REVERT: A 739 LEU cc_start: 0.7945 (tp) cc_final: 0.7722 (tp) REVERT: A 767 PHE cc_start: 0.6022 (m-80) cc_final: 0.5572 (m-80) REVERT: A 862 GLU cc_start: 0.7842 (tp30) cc_final: 0.7476 (tp30) REVERT: A 894 GLU cc_start: 0.6742 (tt0) cc_final: 0.6389 (tt0) REVERT: A 983 TYR cc_start: 0.8841 (m-80) cc_final: 0.7772 (m-80) REVERT: A 1015 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7501 (mt) REVERT: A 1041 THR cc_start: 0.8496 (m) cc_final: 0.7811 (p) REVERT: A 1112 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5797 (p0) REVERT: A 1119 MET cc_start: 0.7817 (mtt) cc_final: 0.7377 (mmp) REVERT: A 1125 ASP cc_start: 0.8170 (t0) cc_final: 0.7825 (t0) REVERT: A 1280 LYS cc_start: 0.6456 (mmtm) cc_final: 0.6008 (tttt) REVERT: A 1294 ARG cc_start: 0.6602 (ttp-110) cc_final: 0.6378 (ttp80) REVERT: A 1308 GLU cc_start: 0.6573 (mp0) cc_final: 0.6080 (mp0) REVERT: A 1346 THR cc_start: 0.8259 (t) cc_final: 0.8007 (p) REVERT: A 1347 SER cc_start: 0.8771 (p) cc_final: 0.8395 (m) REVERT: C 45 ARG cc_start: 0.6315 (ttp-170) cc_final: 0.5741 (ttp-110) REVERT: C 46 TYR cc_start: 0.5759 (m-80) cc_final: 0.5147 (m-80) REVERT: C 79 LYS cc_start: 0.7727 (tppt) cc_final: 0.7510 (tppt) REVERT: C 84 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8310 (t0) REVERT: C 91 MET cc_start: 0.8141 (mtp) cc_final: 0.7899 (mtm) REVERT: C 186 LYS cc_start: 0.6888 (ttpt) cc_final: 0.6580 (tttm) REVERT: C 198 GLU cc_start: 0.7431 (tt0) cc_final: 0.6693 (tm-30) REVERT: C 268 LYS cc_start: 0.7370 (ttpt) cc_final: 0.7131 (ttmm) REVERT: C 369 MET cc_start: 0.7821 (mmt) cc_final: 0.7419 (ptt) REVERT: C 416 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6865 (mp) REVERT: C 477 ARG cc_start: 0.7080 (ttp-110) cc_final: 0.6361 (ptp90) REVERT: C 493 ARG cc_start: 0.8045 (tmm-80) cc_final: 0.7024 (mtm110) REVERT: C 598 LYS cc_start: 0.7040 (ttpp) cc_final: 0.6834 (tptp) REVERT: C 736 ARG cc_start: 0.6757 (mtm-85) cc_final: 0.6353 (mtp85) REVERT: C 909 ASP cc_start: 0.9322 (t70) cc_final: 0.8928 (p0) REVERT: C 912 SER cc_start: 0.8060 (m) cc_final: 0.7794 (p) REVERT: C 915 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.6393 (t-90) REVERT: C 919 ASN cc_start: 0.8007 (t0) cc_final: 0.7077 (m-40) REVERT: C 945 ASN cc_start: 0.7650 (t0) cc_final: 0.7365 (t0) REVERT: C 968 ARG cc_start: 0.7159 (ptm-80) cc_final: 0.6541 (ptt180) REVERT: C 1066 LYS cc_start: 0.8453 (ttpt) cc_final: 0.7454 (tptm) REVERT: C 1159 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.4808 (ptt90) REVERT: C 1199 MET cc_start: 0.7460 (mmt) cc_final: 0.7139 (mmm) REVERT: C 1212 LYS cc_start: 0.6624 (mptt) cc_final: 0.6219 (ttmm) REVERT: C 1219 GLU cc_start: 0.8503 (tp30) cc_final: 0.8236 (tp30) REVERT: C 1244 TYR cc_start: 0.8057 (m-80) cc_final: 0.7438 (m-80) REVERT: 5 25 GLN cc_start: 0.7686 (tt0) cc_final: 0.7051 (pt0) REVERT: 5 89 ARG cc_start: 0.6191 (mtp85) cc_final: 0.5776 (mtp85) REVERT: 5 98 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6646 (p0) REVERT: 5 137 LYS cc_start: 0.6294 (mmtm) cc_final: 0.5719 (mmmt) REVERT: 5 196 LEU cc_start: 0.7916 (tt) cc_final: 0.7649 (tp) REVERT: 5 217 TRP cc_start: 0.6692 (t-100) cc_final: 0.6320 (t-100) REVERT: 5 237 LYS cc_start: 0.6965 (mttt) cc_final: 0.6757 (mmtp) REVERT: 6 26 LYS cc_start: 0.7246 (mtpp) cc_final: 0.7022 (mtmm) REVERT: 6 123 GLU cc_start: 0.7789 (pm20) cc_final: 0.7350 (pm20) REVERT: 6 137 LYS cc_start: 0.6416 (mmtp) cc_final: 0.5989 (mttp) REVERT: 6 187 ASN cc_start: 0.5260 (m-40) cc_final: 0.4954 (m-40) REVERT: 6 211 MET cc_start: 0.6880 (mmm) cc_final: 0.6545 (mtt) REVERT: 6 237 LYS cc_start: 0.6893 (mttt) cc_final: 0.6574 (tptt) REVERT: 6 238 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7175 (mt-10) REVERT: 6 240 ARG cc_start: 0.6274 (ttp-110) cc_final: 0.6007 (ttp-110) REVERT: 6 241 MET cc_start: 0.6209 (mmm) cc_final: 0.5969 (mmp) REVERT: 6 284 GLN cc_start: 0.7324 (pp30) cc_final: 0.6916 (pm20) REVERT: 4 55 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: 4 62 TYR cc_start: 0.5678 (t80) cc_final: 0.5193 (t80) REVERT: 4 152 GLU cc_start: 0.6673 (mp0) cc_final: 0.6412 (mm-30) REVERT: 4 165 GLN cc_start: 0.7977 (pt0) cc_final: 0.7698 (tm-30) REVERT: 4 178 MET cc_start: 0.3579 (mpp) cc_final: 0.3202 (mpp) REVERT: 4 212 ASN cc_start: 0.5268 (m-40) cc_final: 0.4747 (m110) REVERT: 4 280 ASP cc_start: 0.7994 (t0) cc_final: 0.7660 (m-30) REVERT: Z 70 VAL cc_start: 0.5354 (t) cc_final: 0.5084 (t) REVERT: D 19 ARG cc_start: 0.7733 (mmp80) cc_final: 0.7485 (mtp180) REVERT: D 23 ASN cc_start: 0.7060 (m-40) cc_final: 0.6712 (m110) REVERT: p 36 ARG cc_start: 0.6944 (tpp-160) cc_final: 0.6689 (ptm160) REVERT: p 84 LEU cc_start: 0.8168 (tp) cc_final: 0.7837 (tp) REVERT: p 103 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7704 (tm-30) REVERT: p 150 MET cc_start: 0.7361 (mmm) cc_final: 0.6995 (mmm) REVERT: p 153 TYR cc_start: 0.7214 (m-80) cc_final: 0.6467 (m-80) REVERT: p 166 MET cc_start: 0.7454 (mmt) cc_final: 0.7002 (mmm) REVERT: p 222 LYS cc_start: 0.5537 (ptpt) cc_final: 0.5080 (ptpt) REVERT: p 225 ARG cc_start: 0.8637 (tmm-80) cc_final: 0.8164 (tpm170) REVERT: p 226 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7505 (mm-30) REVERT: q 94 VAL cc_start: 0.7810 (m) cc_final: 0.7326 (t) REVERT: q 207 VAL cc_start: 0.7622 (t) cc_final: 0.7384 (t) REVERT: r 4 MET cc_start: 0.4362 (ptm) cc_final: 0.3541 (mmm) REVERT: r 26 LYS cc_start: 0.8876 (mptt) cc_final: 0.8421 (mmmt) REVERT: r 84 HIS cc_start: 0.7372 (t-170) cc_final: 0.7146 (t70) REVERT: r 95 LEU cc_start: 0.8243 (tp) cc_final: 0.7424 (mp) REVERT: r 140 MET cc_start: 0.7735 (tmm) cc_final: 0.7363 (tmm) REVERT: r 163 GLU cc_start: 0.8669 (tt0) cc_final: 0.7762 (mp0) REVERT: r 164 GLU cc_start: 0.8110 (mp0) cc_final: 0.7646 (tm-30) REVERT: r 170 GLN cc_start: 0.8146 (mt0) cc_final: 0.7430 (mp10) REVERT: r 272 PHE cc_start: 0.7181 (m-80) cc_final: 0.6953 (m-80) REVERT: r 276 ARG cc_start: 0.6950 (mtm180) cc_final: 0.6427 (mtm110) REVERT: r 277 GLN cc_start: 0.6389 (tm-30) cc_final: 0.5768 (mm110) outliers start: 226 outliers final: 112 residues processed: 1534 average time/residue: 0.5991 time to fit residues: 1505.7555 Evaluate side-chains 1379 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1249 time to evaluate : 5.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 388 ASN Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 442 PHE Chi-restraints excluded: chain J residue 481 CYS Chi-restraints excluded: chain J residue 495 ILE Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 654 VAL Chi-restraints excluded: chain J residue 760 MET Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 802 LEU Chi-restraints excluded: chain J residue 952 LEU Chi-restraints excluded: chain J residue 1020 LEU Chi-restraints excluded: chain J residue 1048 LEU Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1064 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1113 LEU Chi-restraints excluded: chain J residue 1145 THR Chi-restraints excluded: chain J residue 1181 MET Chi-restraints excluded: chain J residue 1215 TYR Chi-restraints excluded: chain J residue 1242 VAL Chi-restraints excluded: chain J residue 1271 ILE Chi-restraints excluded: chain J residue 1327 THR Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1215 TYR Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 915 HIS Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1159 ARG Chi-restraints excluded: chain C residue 1234 SER Chi-restraints excluded: chain C residue 1327 THR Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 98 ASP Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain 5 residue 162 THR Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 6 residue 37 ILE Chi-restraints excluded: chain 6 residue 57 MET Chi-restraints excluded: chain 6 residue 98 ASP Chi-restraints excluded: chain 6 residue 118 VAL Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 246 ASP Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 4 residue 12 ASP Chi-restraints excluded: chain 4 residue 37 ILE Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 55 GLU Chi-restraints excluded: chain 4 residue 76 VAL Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 137 THR Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain p residue 173 LEU Chi-restraints excluded: chain p residue 202 ILE Chi-restraints excluded: chain p residue 209 ILE Chi-restraints excluded: chain p residue 245 THR Chi-restraints excluded: chain p residue 260 HIS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 110 VAL Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 126 THR Chi-restraints excluded: chain r residue 202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 470 optimal weight: 0.7980 chunk 320 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 421 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 482 optimal weight: 8.9990 chunk 390 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 288 optimal weight: 0.9980 chunk 507 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 199 ASN J 455 HIS J 534 HIS J 618 HIS J1217 HIS J1364 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN A 940 HIS A1133 HIS C 81 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN ** C 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS C 984 HIS ** C1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1223 GLN ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 18 ASN 6 22 HIS ** 6 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 105 HIS ** 6 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 170 ASN 6 248 ASN ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 HIS E 37 HIS ** p 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 88 HIS ** q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 45 GLN ** r 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.9974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 48092 Z= 0.199 Angle : 0.655 9.763 65374 Z= 0.324 Chirality : 0.042 0.341 7563 Planarity : 0.005 0.066 8405 Dihedral : 5.227 65.686 6509 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 4.53 % Allowed : 23.20 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.11), residues: 5871 helix: -0.20 (0.10), residues: 2420 sheet: -1.47 (0.20), residues: 609 loop : -1.02 (0.12), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP p 117 HIS 0.016 0.001 HIS A 940 PHE 0.024 0.001 PHE 4 19 TYR 0.027 0.001 TYR 6 63 ARG 0.011 0.001 ARG A1129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1574 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1339 time to evaluate : 5.221 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: J 25 THR cc_start: 0.5271 (m) cc_final: 0.5066 (m) REVERT: J 80 PHE cc_start: 0.7947 (t80) cc_final: 0.7674 (t80) REVERT: J 81 HIS cc_start: 0.6590 (m-70) cc_final: 0.6123 (m90) REVERT: J 181 GLN cc_start: 0.8225 (mm-40) cc_final: 0.8017 (mm-40) REVERT: J 217 GLN cc_start: 0.7563 (tp40) cc_final: 0.6999 (mt0) REVERT: J 237 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6829 (t70) REVERT: J 310 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5586 (mm-30) REVERT: J 318 TYR cc_start: 0.8545 (m-80) cc_final: 0.8049 (m-80) REVERT: J 382 LYS cc_start: 0.8869 (mmmm) cc_final: 0.7623 (mptt) REVERT: J 388 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7712 (p0) REVERT: J 403 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7386 (mt-10) REVERT: J 439 LYS cc_start: 0.8666 (pttt) cc_final: 0.8076 (tttm) REVERT: J 513 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7614 (mtpt) REVERT: J 682 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7223 (mmt180) REVERT: J 698 LEU cc_start: 0.8949 (mt) cc_final: 0.8692 (mt) REVERT: J 737 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7311 (tp40) REVERT: J 760 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5715 (mtt) REVERT: J 911 ILE cc_start: 0.7960 (mt) cc_final: 0.7707 (mm) REVERT: J 1004 SER cc_start: 0.8273 (t) cc_final: 0.8001 (p) REVERT: J 1046 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6875 (ptp) REVERT: J 1101 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6000 (ptt180) REVERT: J 1190 ASN cc_start: 0.8269 (t0) cc_final: 0.7645 (m110) REVERT: J 1206 ASP cc_start: 0.7214 (t0) cc_final: 0.6927 (t0) REVERT: A 35 LEU cc_start: 0.7246 (pt) cc_final: 0.6867 (pt) REVERT: A 58 CYS cc_start: 0.8041 (p) cc_final: 0.7196 (m) REVERT: A 130 GLU cc_start: 0.7075 (pm20) cc_final: 0.6720 (mt-10) REVERT: A 149 ASP cc_start: 0.6891 (t70) cc_final: 0.6662 (m-30) REVERT: A 150 LYS cc_start: 0.7398 (mmtp) cc_final: 0.6597 (mtpt) REVERT: A 157 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7421 (tpp) REVERT: A 160 VAL cc_start: 0.7870 (t) cc_final: 0.7655 (t) REVERT: A 232 ARG cc_start: 0.7563 (ttm170) cc_final: 0.6571 (mtt-85) REVERT: A 241 LYS cc_start: 0.7419 (ptmm) cc_final: 0.7084 (tttt) REVERT: A 245 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7633 (mtp85) REVERT: A 246 LEU cc_start: 0.7812 (tp) cc_final: 0.7527 (mt) REVERT: A 257 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7244 (p0) REVERT: A 281 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 295 THR cc_start: 0.6966 (p) cc_final: 0.6639 (p) REVERT: A 305 PHE cc_start: 0.6937 (t80) cc_final: 0.6582 (t80) REVERT: A 310 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6244 (mm-30) REVERT: A 326 ASN cc_start: 0.7572 (t0) cc_final: 0.7046 (t0) REVERT: A 329 LYS cc_start: 0.7050 (ttpp) cc_final: 0.6145 (tptm) REVERT: A 336 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 360 ILE cc_start: 0.8492 (tp) cc_final: 0.8144 (tt) REVERT: A 374 ARG cc_start: 0.9037 (ptp90) cc_final: 0.8547 (ptp90) REVERT: A 405 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6500 (mmt-90) REVERT: A 416 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7874 (mt) REVERT: A 498 PHE cc_start: 0.8283 (t80) cc_final: 0.7868 (t80) REVERT: A 538 ASP cc_start: 0.7053 (t0) cc_final: 0.6845 (t0) REVERT: A 701 GLU cc_start: 0.7407 (tt0) cc_final: 0.6854 (mt-10) REVERT: A 739 LEU cc_start: 0.7871 (tp) cc_final: 0.7461 (tp) REVERT: A 767 PHE cc_start: 0.6135 (m-80) cc_final: 0.5721 (m-80) REVERT: A 807 LEU cc_start: 0.6529 (tp) cc_final: 0.6289 (tp) REVERT: A 856 MET cc_start: 0.7971 (tmm) cc_final: 0.7668 (ttp) REVERT: A 894 GLU cc_start: 0.6795 (tt0) cc_final: 0.6462 (tt0) REVERT: A 954 ASP cc_start: 0.6135 (m-30) cc_final: 0.5463 (t70) REVERT: A 958 ARG cc_start: 0.7375 (mtp180) cc_final: 0.6965 (mtp-110) REVERT: A 983 TYR cc_start: 0.8743 (m-80) cc_final: 0.7928 (m-80) REVERT: A 1015 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7577 (mt) REVERT: A 1041 THR cc_start: 0.8390 (m) cc_final: 0.7586 (p) REVERT: A 1069 ARG cc_start: 0.5723 (mtt90) cc_final: 0.5409 (mmt-90) REVERT: A 1119 MET cc_start: 0.7880 (mtt) cc_final: 0.7400 (mmt) REVERT: A 1204 PRO cc_start: 0.8250 (Cg_endo) cc_final: 0.7996 (Cg_exo) REVERT: A 1280 LYS cc_start: 0.6827 (mmtm) cc_final: 0.6368 (tttt) REVERT: A 1308 GLU cc_start: 0.6597 (mp0) cc_final: 0.6073 (mp0) REVERT: A 1346 THR cc_start: 0.8382 (t) cc_final: 0.8134 (p) REVERT: A 1347 SER cc_start: 0.8768 (p) cc_final: 0.8479 (m) REVERT: C 45 ARG cc_start: 0.6382 (ttp-170) cc_final: 0.5853 (ttp-110) REVERT: C 46 TYR cc_start: 0.5616 (m-80) cc_final: 0.5088 (m-80) REVERT: C 79 LYS cc_start: 0.7865 (tppt) cc_final: 0.7584 (ttmm) REVERT: C 91 MET cc_start: 0.8075 (mtp) cc_final: 0.7793 (mtm) REVERT: C 121 GLU cc_start: 0.7248 (tt0) cc_final: 0.6866 (mm-30) REVERT: C 150 LYS cc_start: 0.6477 (mmtp) cc_final: 0.6058 (mmtp) REVERT: C 179 PHE cc_start: 0.7727 (t80) cc_final: 0.7481 (t80) REVERT: C 186 LYS cc_start: 0.7068 (ttpt) cc_final: 0.6838 (tttm) REVERT: C 198 GLU cc_start: 0.7590 (tt0) cc_final: 0.6815 (tm-30) REVERT: C 236 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7183 (ttm-80) REVERT: C 359 VAL cc_start: 0.7777 (t) cc_final: 0.7446 (m) REVERT: C 370 GLU cc_start: 0.7275 (tp30) cc_final: 0.7002 (tp30) REVERT: C 380 ASP cc_start: 0.8407 (t0) cc_final: 0.7967 (p0) REVERT: C 411 GLU cc_start: 0.7794 (pm20) cc_final: 0.7357 (tt0) REVERT: C 416 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6936 (mp) REVERT: C 477 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.6934 (ptp-110) REVERT: C 598 LYS cc_start: 0.7209 (ttpp) cc_final: 0.6891 (tptp) REVERT: C 736 ARG cc_start: 0.6957 (mtm-85) cc_final: 0.6609 (mtp85) REVERT: C 869 HIS cc_start: 0.7491 (p90) cc_final: 0.7175 (p-80) REVERT: C 909 ASP cc_start: 0.9320 (t70) cc_final: 0.8701 (p0) REVERT: C 912 SER cc_start: 0.8088 (m) cc_final: 0.7801 (p) REVERT: C 919 ASN cc_start: 0.7788 (t0) cc_final: 0.6913 (m-40) REVERT: C 945 ASN cc_start: 0.7675 (t0) cc_final: 0.7377 (t0) REVERT: C 967 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.7880 (m-70) REVERT: C 1066 LYS cc_start: 0.8577 (ttpt) cc_final: 0.7721 (tptm) REVERT: C 1113 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5655 (tt) REVERT: C 1125 ASP cc_start: 0.8039 (t0) cc_final: 0.7778 (t0) REVERT: C 1159 ARG cc_start: 0.5407 (OUTLIER) cc_final: 0.5165 (ptt90) REVERT: C 1199 MET cc_start: 0.7573 (mmt) cc_final: 0.7328 (mmt) REVERT: C 1212 LYS cc_start: 0.7314 (mptt) cc_final: 0.6844 (ttmm) REVERT: C 1219 GLU cc_start: 0.8865 (tp30) cc_final: 0.8537 (tp30) REVERT: C 1244 TYR cc_start: 0.8265 (m-80) cc_final: 0.7568 (m-80) REVERT: C 1311 ILE cc_start: 0.8711 (mp) cc_final: 0.7952 (tt) REVERT: 5 25 GLN cc_start: 0.7561 (tt0) cc_final: 0.6998 (pt0) REVERT: 5 46 LEU cc_start: 0.7266 (mt) cc_final: 0.6845 (mp) REVERT: 5 68 PHE cc_start: 0.4788 (t80) cc_final: 0.4537 (t80) REVERT: 5 89 ARG cc_start: 0.6207 (mtp85) cc_final: 0.5766 (mtp85) REVERT: 5 98 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6885 (p0) REVERT: 5 137 LYS cc_start: 0.6294 (mmtm) cc_final: 0.5689 (mmmt) REVERT: 5 175 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.7270 (ttp80) REVERT: 5 237 LYS cc_start: 0.7086 (mttt) cc_final: 0.6873 (mmtp) REVERT: 5 269 GLU cc_start: 0.3600 (mt-10) cc_final: 0.3343 (mt-10) REVERT: 6 99 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.7026 (ttp-110) REVERT: 6 137 LYS cc_start: 0.6812 (mmtp) cc_final: 0.6434 (mttp) REVERT: 6 238 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7169 (mt-10) REVERT: 6 240 ARG cc_start: 0.6466 (ttp-110) cc_final: 0.6220 (ttp-110) REVERT: 6 241 MET cc_start: 0.6246 (mmm) cc_final: 0.6036 (mmp) REVERT: 6 266 THR cc_start: 0.8046 (m) cc_final: 0.7608 (p) REVERT: 6 284 GLN cc_start: 0.7279 (pp30) cc_final: 0.6805 (pm20) REVERT: 4 30 ASP cc_start: 0.7465 (t0) cc_final: 0.7230 (t0) REVERT: 4 43 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7555 (tm-30) REVERT: 4 62 TYR cc_start: 0.5700 (t80) cc_final: 0.5255 (t80) REVERT: 4 111 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.5298 (mtp85) REVERT: 4 212 ASN cc_start: 0.5834 (m-40) cc_final: 0.5340 (m110) REVERT: 4 221 GLU cc_start: 0.6768 (tt0) cc_final: 0.6503 (mm-30) REVERT: Z 49 ARG cc_start: 0.8428 (mmt90) cc_final: 0.7887 (mtm180) REVERT: D 63 ASP cc_start: 0.6125 (t70) cc_final: 0.5869 (t70) REVERT: p 84 LEU cc_start: 0.8098 (tp) cc_final: 0.7747 (tp) REVERT: p 150 MET cc_start: 0.7282 (mmm) cc_final: 0.6933 (mmm) REVERT: p 153 TYR cc_start: 0.7316 (m-80) cc_final: 0.6518 (m-80) REVERT: p 166 MET cc_start: 0.7328 (mmt) cc_final: 0.6924 (mmm) REVERT: q 4 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6792 (mtm) REVERT: q 94 VAL cc_start: 0.7648 (m) cc_final: 0.7355 (t) REVERT: q 171 GLN cc_start: 0.8020 (pp30) cc_final: 0.7648 (pp30) REVERT: q 207 VAL cc_start: 0.7666 (t) cc_final: 0.7404 (t) REVERT: q 218 TYR cc_start: 0.8651 (t80) cc_final: 0.8169 (t80) REVERT: q 239 MET cc_start: 0.7078 (tmm) cc_final: 0.6861 (tmm) REVERT: r 4 MET cc_start: 0.4130 (ptm) cc_final: 0.3444 (mmm) REVERT: r 15 LYS cc_start: 0.6953 (pptt) cc_final: 0.6709 (pttp) REVERT: r 26 LYS cc_start: 0.8823 (mptt) cc_final: 0.8321 (mmmt) REVERT: r 37 ARG cc_start: 0.4770 (mtm110) cc_final: 0.4048 (mtt-85) REVERT: r 95 LEU cc_start: 0.8366 (tp) cc_final: 0.7613 (mp) REVERT: r 140 MET cc_start: 0.7846 (tmm) cc_final: 0.7571 (tmm) REVERT: r 163 GLU cc_start: 0.8535 (tt0) cc_final: 0.7567 (mp0) REVERT: r 164 GLU cc_start: 0.8134 (mp0) cc_final: 0.7700 (tm-30) REVERT: r 170 GLN cc_start: 0.8372 (mt0) cc_final: 0.7799 (mp10) REVERT: r 225 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.5152 (tm-30) REVERT: r 230 LEU cc_start: 0.7356 (tp) cc_final: 0.6917 (tp) REVERT: r 233 LYS cc_start: 0.7973 (tptm) cc_final: 0.7334 (ttmt) REVERT: r 284 GLU cc_start: 0.6111 (tm-30) cc_final: 0.5559 (mm-30) REVERT: r 294 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7489 (p) outliers start: 235 outliers final: 136 residues processed: 1470 average time/residue: 0.5895 time to fit residues: 1426.6674 Evaluate side-chains 1407 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1253 time to evaluate : 5.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 369 MET Chi-restraints excluded: chain J residue 388 ASN Chi-restraints excluded: chain J residue 414 VAL Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 440 ILE Chi-restraints excluded: chain J residue 481 CYS Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 573 LEU Chi-restraints excluded: chain J residue 654 VAL Chi-restraints excluded: chain J residue 754 VAL Chi-restraints excluded: chain J residue 760 MET Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 925 THR Chi-restraints excluded: chain J residue 942 PHE Chi-restraints excluded: chain J residue 945 ASN Chi-restraints excluded: chain J residue 952 LEU Chi-restraints excluded: chain J residue 1046 MET Chi-restraints excluded: chain J residue 1048 LEU Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1064 VAL Chi-restraints excluded: chain J residue 1096 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1145 THR Chi-restraints excluded: chain J residue 1172 CYS Chi-restraints excluded: chain J residue 1181 MET Chi-restraints excluded: chain J residue 1242 VAL Chi-restraints excluded: chain J residue 1312 GLU Chi-restraints excluded: chain J residue 1327 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1328 THR Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 914 GLN Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1159 ARG Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1234 SER Chi-restraints excluded: chain C residue 1262 CYS Chi-restraints excluded: chain C residue 1292 CYS Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain 5 residue 98 ASP Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 162 THR Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 6 residue 98 ASP Chi-restraints excluded: chain 6 residue 151 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 211 MET Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 4 residue 20 LEU Chi-restraints excluded: chain 4 residue 37 ILE Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 76 VAL Chi-restraints excluded: chain 4 residue 206 THR Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain p residue 161 GLU Chi-restraints excluded: chain p residue 173 LEU Chi-restraints excluded: chain p residue 183 GLN Chi-restraints excluded: chain p residue 202 ILE Chi-restraints excluded: chain p residue 245 THR Chi-restraints excluded: chain p residue 260 HIS Chi-restraints excluded: chain p residue 261 THR Chi-restraints excluded: chain q residue 4 MET Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain q residue 110 VAL Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain q residue 201 CYS Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 126 THR Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 225 GLU Chi-restraints excluded: chain r residue 294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 190 optimal weight: 0.0670 chunk 509 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 139 optimal weight: 0.0030 chunk 566 optimal weight: 0.0030 chunk 469 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 47 optimal weight: 0.0980 chunk 187 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 153 ASN J 199 ASN J 455 HIS J 637 ASN A 211 GLN A 231 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 HIS A1267 ASN C 76 HIS C 81 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN C 514 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 649 HIS C 722 HIS C1003 HIS ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN ** C1217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 105 HIS 6 18 ASN ** 6 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 260 ASN E 37 HIS ** p 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 209 ASN ** r 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 1.0143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 48092 Z= 0.161 Angle : 0.622 9.934 65374 Z= 0.305 Chirality : 0.040 0.352 7563 Planarity : 0.004 0.068 8405 Dihedral : 4.956 62.684 6509 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 3.86 % Allowed : 24.32 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.11), residues: 5871 helix: 0.08 (0.11), residues: 2429 sheet: -1.31 (0.20), residues: 613 loop : -0.96 (0.12), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP p 117 HIS 0.026 0.001 HIS E 37 PHE 0.022 0.001 PHE C 880 TYR 0.022 0.001 TYR C 38 ARG 0.013 0.000 ARG C1038 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1315 time to evaluate : 5.880 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: J 25 THR cc_start: 0.5483 (m) cc_final: 0.5279 (m) REVERT: J 81 HIS cc_start: 0.6722 (m-70) cc_final: 0.6397 (m90) REVERT: J 217 GLN cc_start: 0.7484 (tp40) cc_final: 0.6950 (mt0) REVERT: J 237 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6821 (t70) REVERT: J 310 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5608 (mm-30) REVERT: J 382 LYS cc_start: 0.8348 (mmmm) cc_final: 0.7705 (mptt) REVERT: J 388 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7879 (p0) REVERT: J 403 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7447 (mt-10) REVERT: J 439 LYS cc_start: 0.8447 (pttt) cc_final: 0.7984 (tttm) REVERT: J 513 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7524 (mtpt) REVERT: J 682 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.7266 (mmt180) REVERT: J 698 LEU cc_start: 0.8936 (mt) cc_final: 0.8704 (mt) REVERT: J 737 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7177 (tp40) REVERT: J 911 ILE cc_start: 0.8039 (mt) cc_final: 0.7810 (mm) REVERT: J 915 HIS cc_start: 0.7247 (m-70) cc_final: 0.6425 (m-70) REVERT: J 979 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.5643 (m-80) REVERT: J 1004 SER cc_start: 0.8259 (t) cc_final: 0.7975 (p) REVERT: J 1046 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6905 (ptp) REVERT: J 1113 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7021 (mp) REVERT: J 1115 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7762 (mtp85) REVERT: J 1117 PHE cc_start: 0.7695 (m-80) cc_final: 0.7372 (m-10) REVERT: J 1190 ASN cc_start: 0.8168 (t0) cc_final: 0.7577 (m110) REVERT: J 1206 ASP cc_start: 0.7230 (t0) cc_final: 0.6842 (t0) REVERT: A 35 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6814 (pt) REVERT: A 41 ASP cc_start: 0.5913 (p0) cc_final: 0.5397 (m-30) REVERT: A 58 CYS cc_start: 0.7963 (p) cc_final: 0.7016 (m) REVERT: A 130 GLU cc_start: 0.7094 (pm20) cc_final: 0.6815 (mt-10) REVERT: A 149 ASP cc_start: 0.6887 (t70) cc_final: 0.6662 (m-30) REVERT: A 150 LYS cc_start: 0.7420 (mmtp) cc_final: 0.6543 (mtpt) REVERT: A 157 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7432 (tpp) REVERT: A 160 VAL cc_start: 0.7820 (t) cc_final: 0.7574 (t) REVERT: A 232 ARG cc_start: 0.7774 (ttm170) cc_final: 0.6576 (mtt-85) REVERT: A 241 LYS cc_start: 0.7429 (ptmm) cc_final: 0.7119 (tttt) REVERT: A 245 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7658 (mtp85) REVERT: A 246 LEU cc_start: 0.7782 (tp) cc_final: 0.7502 (mt) REVERT: A 257 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7384 (p0) REVERT: A 281 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 295 THR cc_start: 0.7036 (p) cc_final: 0.6719 (p) REVERT: A 305 PHE cc_start: 0.6937 (t80) cc_final: 0.6673 (t80) REVERT: A 310 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6459 (mm-30) REVERT: A 326 ASN cc_start: 0.7375 (t0) cc_final: 0.6853 (t0) REVERT: A 329 LYS cc_start: 0.7000 (ttpp) cc_final: 0.6104 (tptm) REVERT: A 336 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 360 ILE cc_start: 0.8550 (tp) cc_final: 0.8097 (tt) REVERT: A 374 ARG cc_start: 0.9039 (ptp90) cc_final: 0.8585 (ptp90) REVERT: A 405 ARG cc_start: 0.7183 (mtm-85) cc_final: 0.6515 (mmt-90) REVERT: A 416 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7727 (mt) REVERT: A 498 PHE cc_start: 0.8245 (t80) cc_final: 0.7796 (t80) REVERT: A 538 ASP cc_start: 0.7105 (t0) cc_final: 0.6757 (t0) REVERT: A 551 LEU cc_start: 0.8251 (tt) cc_final: 0.8042 (tt) REVERT: A 701 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6644 (mt-10) REVERT: A 739 LEU cc_start: 0.7880 (tp) cc_final: 0.7658 (tp) REVERT: A 767 PHE cc_start: 0.6241 (m-80) cc_final: 0.5917 (m-80) REVERT: A 894 GLU cc_start: 0.6741 (tt0) cc_final: 0.6403 (tt0) REVERT: A 954 ASP cc_start: 0.6121 (m-30) cc_final: 0.5339 (t70) REVERT: A 957 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7918 (tttm) REVERT: A 958 ARG cc_start: 0.7210 (mtp180) cc_final: 0.6807 (mtp-110) REVERT: A 983 TYR cc_start: 0.8713 (m-80) cc_final: 0.7850 (m-80) REVERT: A 1015 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7720 (mt) REVERT: A 1041 THR cc_start: 0.8424 (m) cc_final: 0.7628 (p) REVERT: A 1069 ARG cc_start: 0.5771 (mtt90) cc_final: 0.5441 (mmt-90) REVERT: A 1119 MET cc_start: 0.7789 (mtt) cc_final: 0.7385 (mmt) REVERT: A 1129 ARG cc_start: 0.6476 (mtm-85) cc_final: 0.6252 (mtm110) REVERT: A 1204 PRO cc_start: 0.8149 (Cg_endo) cc_final: 0.7901 (Cg_exo) REVERT: A 1207 THR cc_start: 0.7927 (m) cc_final: 0.7713 (p) REVERT: A 1280 LYS cc_start: 0.6524 (mmtm) cc_final: 0.6122 (tttt) REVERT: A 1308 GLU cc_start: 0.6683 (mp0) cc_final: 0.6140 (mp0) REVERT: A 1346 THR cc_start: 0.8420 (t) cc_final: 0.8220 (p) REVERT: A 1347 SER cc_start: 0.8754 (p) cc_final: 0.8526 (m) REVERT: C 36 ARG cc_start: 0.7282 (ttp80) cc_final: 0.6957 (ttt90) REVERT: C 38 TYR cc_start: 0.8410 (p90) cc_final: 0.8070 (p90) REVERT: C 45 ARG cc_start: 0.6351 (ttp-170) cc_final: 0.5840 (ttp-110) REVERT: C 46 TYR cc_start: 0.5932 (m-80) cc_final: 0.5376 (m-80) REVERT: C 79 LYS cc_start: 0.7840 (tppt) cc_final: 0.7492 (ttmm) REVERT: C 150 LYS cc_start: 0.6400 (mmtp) cc_final: 0.5964 (mmtp) REVERT: C 179 PHE cc_start: 0.7388 (t80) cc_final: 0.7125 (t80) REVERT: C 186 LYS cc_start: 0.7046 (ttpt) cc_final: 0.6812 (tttm) REVERT: C 198 GLU cc_start: 0.7572 (tt0) cc_final: 0.6962 (tm-30) REVERT: C 284 MET cc_start: 0.7605 (mmp) cc_final: 0.6679 (mmp) REVERT: C 380 ASP cc_start: 0.8400 (t0) cc_final: 0.7954 (p0) REVERT: C 411 GLU cc_start: 0.7843 (pm20) cc_final: 0.7412 (tt0) REVERT: C 416 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.6973 (mp) REVERT: C 453 VAL cc_start: 0.8834 (p) cc_final: 0.8536 (m) REVERT: C 512 MET cc_start: 0.6510 (mtm) cc_final: 0.6300 (mtm) REVERT: C 598 LYS cc_start: 0.7135 (ttpp) cc_final: 0.6873 (tptp) REVERT: C 736 ARG cc_start: 0.6934 (mtm-85) cc_final: 0.6650 (mtp85) REVERT: C 869 HIS cc_start: 0.7508 (p90) cc_final: 0.6850 (p-80) REVERT: C 909 ASP cc_start: 0.9363 (t70) cc_final: 0.8728 (p0) REVERT: C 912 SER cc_start: 0.8121 (m) cc_final: 0.7844 (p) REVERT: C 919 ASN cc_start: 0.7722 (t0) cc_final: 0.6919 (m-40) REVERT: C 945 ASN cc_start: 0.7708 (t0) cc_final: 0.7401 (t0) REVERT: C 960 VAL cc_start: 0.6768 (t) cc_final: 0.6535 (t) REVERT: C 967 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7736 (t70) REVERT: C 968 ARG cc_start: 0.7346 (ptm-80) cc_final: 0.6416 (ptt180) REVERT: C 1066 LYS cc_start: 0.8582 (ttpt) cc_final: 0.7751 (tptm) REVERT: C 1113 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5598 (tt) REVERT: C 1125 ASP cc_start: 0.8042 (t0) cc_final: 0.7786 (t0) REVERT: C 1159 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.5510 (ptt90) REVERT: C 1199 MET cc_start: 0.7574 (mmt) cc_final: 0.7325 (mmt) REVERT: C 1212 LYS cc_start: 0.7303 (mptt) cc_final: 0.6821 (ttmm) REVERT: C 1219 GLU cc_start: 0.8877 (tp30) cc_final: 0.8517 (tp30) REVERT: C 1244 TYR cc_start: 0.8109 (m-80) cc_final: 0.7271 (m-80) REVERT: 5 25 GLN cc_start: 0.7758 (tt0) cc_final: 0.7288 (pt0) REVERT: 5 26 LYS cc_start: 0.5945 (mttm) cc_final: 0.5492 (mtmm) REVERT: 5 46 LEU cc_start: 0.7490 (mt) cc_final: 0.7244 (mp) REVERT: 5 68 PHE cc_start: 0.4828 (t80) cc_final: 0.4574 (t80) REVERT: 5 89 ARG cc_start: 0.6157 (mtp85) cc_final: 0.5744 (mtp85) REVERT: 5 98 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6690 (p0) REVERT: 5 137 LYS cc_start: 0.6329 (mmtm) cc_final: 0.5727 (mmmt) REVERT: 5 175 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.7213 (ttp80) REVERT: 5 217 TRP cc_start: 0.6803 (t-100) cc_final: 0.6568 (t-100) REVERT: 5 234 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6238 (mp) REVERT: 5 237 LYS cc_start: 0.7058 (mttt) cc_final: 0.6806 (mmtp) REVERT: 5 238 GLU cc_start: 0.6663 (mm-30) cc_final: 0.6422 (mm-30) REVERT: 6 26 LYS cc_start: 0.7606 (mtmm) cc_final: 0.6986 (mtmm) REVERT: 6 137 LYS cc_start: 0.6958 (mmtp) cc_final: 0.6455 (mttp) REVERT: 6 238 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6354 (tp30) REVERT: 6 240 ARG cc_start: 0.6567 (ttp-110) cc_final: 0.6354 (ttp-110) REVERT: 6 241 MET cc_start: 0.6415 (mmm) cc_final: 0.6186 (mmp) REVERT: 6 266 THR cc_start: 0.8060 (m) cc_final: 0.7633 (p) REVERT: 6 271 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6499 (tp) REVERT: 6 273 GLU cc_start: 0.6813 (tp30) cc_final: 0.6144 (tt0) REVERT: 6 284 GLN cc_start: 0.7222 (pp30) cc_final: 0.6835 (pm20) REVERT: 4 30 ASP cc_start: 0.7418 (t0) cc_final: 0.7217 (t0) REVERT: 4 55 GLU cc_start: 0.7697 (mp0) cc_final: 0.7205 (mp0) REVERT: 4 62 TYR cc_start: 0.5729 (t80) cc_final: 0.5184 (t80) REVERT: 4 111 ARG cc_start: 0.6368 (mtp-110) cc_final: 0.6153 (mtp-110) REVERT: 4 165 GLN cc_start: 0.7986 (pt0) cc_final: 0.7665 (tm-30) REVERT: 4 212 ASN cc_start: 0.5907 (m-40) cc_final: 0.5085 (m110) REVERT: 4 221 GLU cc_start: 0.6789 (tt0) cc_final: 0.6385 (mm-30) REVERT: Z 49 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7471 (mtm180) REVERT: D 37 HIS cc_start: 0.5798 (OUTLIER) cc_final: 0.4982 (t-90) REVERT: E 17 LYS cc_start: 0.7300 (mmmt) cc_final: 0.7087 (mmmm) REVERT: p 84 LEU cc_start: 0.8194 (tp) cc_final: 0.7864 (tp) REVERT: p 89 ILE cc_start: 0.7304 (tt) cc_final: 0.6829 (tt) REVERT: p 150 MET cc_start: 0.7261 (mmm) cc_final: 0.7019 (mmm) REVERT: p 153 TYR cc_start: 0.7237 (m-80) cc_final: 0.6562 (m-80) REVERT: p 166 MET cc_start: 0.7378 (mmt) cc_final: 0.7109 (mmm) REVERT: p 225 ARG cc_start: 0.8832 (tmm-80) cc_final: 0.8044 (tpm170) REVERT: q 80 GLN cc_start: 0.8657 (tt0) cc_final: 0.7913 (tp40) REVERT: q 94 VAL cc_start: 0.7374 (m) cc_final: 0.6932 (t) REVERT: q 140 MET cc_start: 0.7820 (tpt) cc_final: 0.7571 (tpt) REVERT: q 171 GLN cc_start: 0.8077 (pp30) cc_final: 0.7698 (pp30) REVERT: q 218 TYR cc_start: 0.8606 (t80) cc_final: 0.8054 (t80) REVERT: r 4 MET cc_start: 0.4095 (ptm) cc_final: 0.3429 (mmm) REVERT: r 15 LYS cc_start: 0.7007 (pptt) cc_final: 0.6774 (pttp) REVERT: r 26 LYS cc_start: 0.8840 (mptt) cc_final: 0.8333 (mmmt) REVERT: r 37 ARG cc_start: 0.4842 (mtm110) cc_final: 0.4082 (mtt-85) REVERT: r 95 LEU cc_start: 0.8232 (tp) cc_final: 0.7501 (mp) REVERT: r 140 MET cc_start: 0.7827 (tmm) cc_final: 0.7544 (tmm) REVERT: r 156 PHE cc_start: 0.7382 (m-80) cc_final: 0.7168 (m-80) REVERT: r 163 GLU cc_start: 0.8517 (tt0) cc_final: 0.7606 (mp0) REVERT: r 164 GLU cc_start: 0.8226 (mp0) cc_final: 0.7823 (tm-30) REVERT: r 170 GLN cc_start: 0.8384 (mt0) cc_final: 0.7859 (mp10) REVERT: r 175 ILE cc_start: 0.7846 (tp) cc_final: 0.7560 (tp) REVERT: r 233 LYS cc_start: 0.7975 (tptm) cc_final: 0.7742 (tptm) REVERT: r 277 GLN cc_start: 0.6598 (tm-30) cc_final: 0.6253 (tm-30) REVERT: r 297 ASN cc_start: 0.7895 (m-40) cc_final: 0.7135 (t0) outliers start: 200 outliers final: 124 residues processed: 1419 average time/residue: 0.5852 time to fit residues: 1373.6134 Evaluate side-chains 1392 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1248 time to evaluate : 5.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 388 ASN Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 594 LEU Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 892 VAL Chi-restraints excluded: chain J residue 900 ASP Chi-restraints excluded: chain J residue 942 PHE Chi-restraints excluded: chain J residue 952 LEU Chi-restraints excluded: chain J residue 979 PHE Chi-restraints excluded: chain J residue 1046 MET Chi-restraints excluded: chain J residue 1048 LEU Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1064 VAL Chi-restraints excluded: chain J residue 1105 ASP Chi-restraints excluded: chain J residue 1113 LEU Chi-restraints excluded: chain J residue 1172 CYS Chi-restraints excluded: chain J residue 1181 MET Chi-restraints excluded: chain J residue 1242 VAL Chi-restraints excluded: chain J residue 1312 GLU Chi-restraints excluded: chain J residue 1327 THR Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1328 THR Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 914 GLN Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1106 MET Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1159 ARG Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1234 SER Chi-restraints excluded: chain C residue 1292 CYS Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain 5 residue 98 ASP Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 162 THR Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 5 residue 234 LEU Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 276 ASP Chi-restraints excluded: chain 6 residue 151 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 242 CYS Chi-restraints excluded: chain 6 residue 246 ASP Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 76 VAL Chi-restraints excluded: chain 4 residue 222 ARG Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain p residue 173 LEU Chi-restraints excluded: chain p residue 183 GLN Chi-restraints excluded: chain p residue 202 ILE Chi-restraints excluded: chain p residue 205 LEU Chi-restraints excluded: chain p residue 245 THR Chi-restraints excluded: chain p residue 260 HIS Chi-restraints excluded: chain p residue 261 THR Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 74 ARG Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain q residue 110 VAL Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain q residue 201 CYS Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 126 THR Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 244 GLU Chi-restraints excluded: chain r residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 545 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 322 optimal weight: 8.9990 chunk 413 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 476 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 563 optimal weight: 0.0670 chunk 352 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 HIS ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 HIS A1217 HIS A1267 ASN C 81 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 HIS ** C 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1353 ASN ** C1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 18 ASN ** 6 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 170 ASN ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** p 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 1.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 48092 Z= 0.240 Angle : 0.665 10.945 65374 Z= 0.331 Chirality : 0.042 0.407 7563 Planarity : 0.005 0.066 8405 Dihedral : 4.967 64.642 6509 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 4.74 % Allowed : 23.62 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.11), residues: 5871 helix: 0.04 (0.10), residues: 2444 sheet: -1.30 (0.20), residues: 650 loop : -0.95 (0.12), residues: 2777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP p 117 HIS 0.053 0.001 HIS E 37 PHE 0.025 0.002 PHE 4 53 TYR 0.022 0.001 TYR J1215 ARG 0.008 0.001 ARG C1038 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1615 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1369 time to evaluate : 4.987 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: J 25 THR cc_start: 0.5355 (m) cc_final: 0.5057 (m) REVERT: J 96 GLN cc_start: 0.7970 (mt0) cc_final: 0.7517 (mt0) REVERT: J 125 ILE cc_start: 0.7956 (pt) cc_final: 0.7305 (pt) REVERT: J 141 GLU cc_start: 0.7297 (tm-30) cc_final: 0.7054 (tp30) REVERT: J 217 GLN cc_start: 0.7776 (tp40) cc_final: 0.7327 (mt0) REVERT: J 237 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6825 (p0) REVERT: J 310 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5934 (mm-30) REVERT: J 353 THR cc_start: 0.7954 (t) cc_final: 0.7733 (m) REVERT: J 382 LYS cc_start: 0.8520 (mmmm) cc_final: 0.7846 (mptt) REVERT: J 388 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8008 (p0) REVERT: J 403 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7487 (mt-10) REVERT: J 404 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.7794 (t0) REVERT: J 439 LYS cc_start: 0.8464 (pttt) cc_final: 0.7936 (tttm) REVERT: J 513 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7938 (mtpt) REVERT: J 634 CYS cc_start: 0.6609 (m) cc_final: 0.6374 (m) REVERT: J 682 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7471 (mmt180) REVERT: J 737 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7450 (tp40) REVERT: J 815 PRO cc_start: 0.8319 (Cg_exo) cc_final: 0.8066 (Cg_endo) REVERT: J 900 ASP cc_start: 0.6191 (p0) cc_final: 0.5938 (p0) REVERT: J 911 ILE cc_start: 0.8236 (mt) cc_final: 0.8020 (mm) REVERT: J 979 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6238 (m-80) REVERT: J 1004 SER cc_start: 0.8223 (t) cc_final: 0.7897 (p) REVERT: J 1023 GLN cc_start: 0.7575 (mt0) cc_final: 0.7284 (mt0) REVERT: J 1046 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7351 (ptp) REVERT: J 1101 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6443 (ptt180) REVERT: J 1115 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7752 (mtp85) REVERT: J 1117 PHE cc_start: 0.7846 (m-80) cc_final: 0.7563 (m-10) REVERT: J 1129 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7964 (ttm110) REVERT: J 1190 ASN cc_start: 0.8039 (t0) cc_final: 0.7571 (m110) REVERT: J 1206 ASP cc_start: 0.7618 (t0) cc_final: 0.7382 (t0) REVERT: J 1208 GLU cc_start: 0.8168 (tp30) cc_final: 0.7647 (pm20) REVERT: J 1280 LYS cc_start: 0.8209 (tptt) cc_final: 0.7801 (tppt) REVERT: A 35 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7155 (pt) REVERT: A 41 ASP cc_start: 0.6058 (p0) cc_final: 0.5770 (m-30) REVERT: A 58 CYS cc_start: 0.8172 (p) cc_final: 0.7224 (m) REVERT: A 67 LEU cc_start: 0.8197 (mt) cc_final: 0.7564 (mp) REVERT: A 149 ASP cc_start: 0.7514 (t70) cc_final: 0.7256 (m-30) REVERT: A 157 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7387 (tpp) REVERT: A 160 VAL cc_start: 0.7967 (t) cc_final: 0.7706 (t) REVERT: A 232 ARG cc_start: 0.7784 (ttm170) cc_final: 0.6630 (mtt-85) REVERT: A 241 LYS cc_start: 0.8061 (ptmm) cc_final: 0.7792 (tttt) REVERT: A 245 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7729 (mtp85) REVERT: A 257 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7235 (p0) REVERT: A 281 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 295 THR cc_start: 0.7252 (p) cc_final: 0.6942 (p) REVERT: A 310 GLU cc_start: 0.7704 (mt-10) cc_final: 0.6708 (mm-30) REVERT: A 326 ASN cc_start: 0.7419 (t0) cc_final: 0.6932 (t0) REVERT: A 329 LYS cc_start: 0.7012 (ttpp) cc_final: 0.5851 (tptt) REVERT: A 336 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 360 ILE cc_start: 0.8690 (tp) cc_final: 0.8204 (tt) REVERT: A 369 MET cc_start: 0.7774 (mtp) cc_final: 0.7471 (mtp) REVERT: A 374 ARG cc_start: 0.9033 (ptp90) cc_final: 0.8793 (ptp90) REVERT: A 382 LYS cc_start: 0.8419 (tptt) cc_final: 0.7020 (mptt) REVERT: A 397 VAL cc_start: 0.8253 (t) cc_final: 0.8034 (t) REVERT: A 405 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.6493 (mmt-90) REVERT: A 416 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7942 (mt) REVERT: A 551 LEU cc_start: 0.8351 (tt) cc_final: 0.8137 (tt) REVERT: A 701 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: A 767 PHE cc_start: 0.6398 (m-80) cc_final: 0.6063 (m-80) REVERT: A 807 LEU cc_start: 0.6562 (tp) cc_final: 0.6224 (tp) REVERT: A 856 MET cc_start: 0.8580 (tmm) cc_final: 0.8379 (tmm) REVERT: A 954 ASP cc_start: 0.6937 (m-30) cc_final: 0.6352 (t0) REVERT: A 957 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8060 (tttm) REVERT: A 983 TYR cc_start: 0.8651 (m-80) cc_final: 0.8314 (m-80) REVERT: A 1015 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7581 (mt) REVERT: A 1041 THR cc_start: 0.8517 (m) cc_final: 0.7782 (p) REVERT: A 1069 ARG cc_start: 0.5929 (mtt90) cc_final: 0.5603 (mmt-90) REVERT: A 1098 TYR cc_start: 0.8249 (t80) cc_final: 0.7994 (t80) REVERT: A 1119 MET cc_start: 0.7816 (mtt) cc_final: 0.7421 (mmt) REVERT: A 1207 THR cc_start: 0.7977 (m) cc_final: 0.7731 (p) REVERT: A 1267 ASN cc_start: 0.8533 (m-40) cc_final: 0.8274 (m110) REVERT: A 1280 LYS cc_start: 0.6931 (mmtm) cc_final: 0.6392 (tttp) REVERT: A 1308 GLU cc_start: 0.6352 (mp0) cc_final: 0.5897 (mp0) REVERT: A 1320 GLU cc_start: 0.7655 (pp20) cc_final: 0.6918 (pp20) REVERT: C 23 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7888 (m) REVERT: C 30 GLU cc_start: 0.8366 (tt0) cc_final: 0.8035 (tt0) REVERT: C 36 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7367 (ttt90) REVERT: C 45 ARG cc_start: 0.6362 (ttp-170) cc_final: 0.6065 (ttp-110) REVERT: C 46 TYR cc_start: 0.5607 (m-80) cc_final: 0.5155 (m-80) REVERT: C 121 GLU cc_start: 0.7365 (tt0) cc_final: 0.6981 (mm-30) REVERT: C 137 THR cc_start: 0.8353 (t) cc_final: 0.7991 (p) REVERT: C 150 LYS cc_start: 0.6439 (mmtp) cc_final: 0.6011 (mmtp) REVERT: C 186 LYS cc_start: 0.7462 (ttpt) cc_final: 0.7233 (tttm) REVERT: C 276 THR cc_start: 0.7452 (m) cc_final: 0.7235 (p) REVERT: C 310 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7226 (mt-10) REVERT: C 380 ASP cc_start: 0.8219 (t0) cc_final: 0.7915 (p0) REVERT: C 411 GLU cc_start: 0.7956 (pm20) cc_final: 0.7603 (tt0) REVERT: C 453 VAL cc_start: 0.8767 (p) cc_final: 0.8440 (m) REVERT: C 598 LYS cc_start: 0.7316 (ttpp) cc_final: 0.6970 (tptm) REVERT: C 608 GLU cc_start: 0.6409 (mp0) cc_final: 0.6133 (mp0) REVERT: C 736 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6774 (mtp85) REVERT: C 909 ASP cc_start: 0.9409 (t70) cc_final: 0.8778 (p0) REVERT: C 912 SER cc_start: 0.8333 (m) cc_final: 0.8115 (p) REVERT: C 919 ASN cc_start: 0.7670 (t0) cc_final: 0.6860 (m-40) REVERT: C 945 ASN cc_start: 0.7646 (t0) cc_final: 0.7308 (t0) REVERT: C 1066 LYS cc_start: 0.8615 (ttpt) cc_final: 0.7764 (tptm) REVERT: C 1069 ARG cc_start: 0.6187 (mmm-85) cc_final: 0.5807 (mtp85) REVERT: C 1125 ASP cc_start: 0.8201 (t0) cc_final: 0.7911 (t0) REVERT: C 1129 ARG cc_start: 0.6943 (mmt-90) cc_final: 0.6434 (mpt180) REVERT: C 1159 ARG cc_start: 0.5747 (OUTLIER) cc_final: 0.5530 (ptt90) REVERT: C 1174 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5262 (mt) REVERT: C 1212 LYS cc_start: 0.7517 (mptt) cc_final: 0.7180 (ttmm) REVERT: C 1225 PHE cc_start: 0.8739 (m-80) cc_final: 0.8537 (m-80) REVERT: C 1235 GLN cc_start: 0.6661 (tp40) cc_final: 0.6361 (tp40) REVERT: C 1244 TYR cc_start: 0.8445 (m-80) cc_final: 0.7436 (m-80) REVERT: C 1348 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8531 (mm-30) REVERT: C 1358 GLU cc_start: 0.6537 (pt0) cc_final: 0.6216 (pt0) REVERT: 5 25 GLN cc_start: 0.7853 (tt0) cc_final: 0.7298 (pt0) REVERT: 5 46 LEU cc_start: 0.7728 (mt) cc_final: 0.7456 (mp) REVERT: 5 89 ARG cc_start: 0.6261 (mtp85) cc_final: 0.5919 (mtp85) REVERT: 5 98 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6751 (p0) REVERT: 5 137 LYS cc_start: 0.6364 (mmtm) cc_final: 0.5753 (mmmt) REVERT: 5 175 ARG cc_start: 0.7555 (ttp-110) cc_final: 0.7317 (ttp80) REVERT: 5 234 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6693 (mp) REVERT: 5 269 GLU cc_start: 0.4100 (mt-10) cc_final: 0.3784 (mt-10) REVERT: 5 280 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7653 (t0) REVERT: 6 26 LYS cc_start: 0.7638 (mtmm) cc_final: 0.7019 (mtmm) REVERT: 6 101 LYS cc_start: 0.8378 (tmtt) cc_final: 0.8101 (tttp) REVERT: 6 178 MET cc_start: 0.6739 (pmm) cc_final: 0.5712 (pmm) REVERT: 6 182 LYS cc_start: 0.7654 (mtmm) cc_final: 0.6351 (mmpt) REVERT: 6 240 ARG cc_start: 0.6597 (ttp-110) cc_final: 0.6172 (ttp-110) REVERT: 6 266 THR cc_start: 0.8138 (m) cc_final: 0.7711 (p) REVERT: 6 271 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6608 (tp) REVERT: 6 273 GLU cc_start: 0.6927 (tp30) cc_final: 0.6172 (tt0) REVERT: 6 284 GLN cc_start: 0.7153 (pp30) cc_final: 0.6900 (pm20) REVERT: 4 55 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: 4 57 MET cc_start: 0.7013 (ttt) cc_final: 0.6757 (tpp) REVERT: 4 211 MET cc_start: 0.6266 (tmm) cc_final: 0.6064 (ttt) REVERT: 4 212 ASN cc_start: 0.6043 (m-40) cc_final: 0.4877 (m-40) REVERT: 4 218 GLU cc_start: 0.6529 (tm-30) cc_final: 0.5930 (mt-10) REVERT: 4 233 LYS cc_start: 0.7189 (tptp) cc_final: 0.6427 (mmtm) REVERT: 4 238 GLU cc_start: 0.8394 (tp30) cc_final: 0.8186 (tp30) REVERT: 4 241 MET cc_start: 0.5914 (mtm) cc_final: 0.5645 (mmt) REVERT: Z 49 ARG cc_start: 0.8098 (mmt90) cc_final: 0.7586 (mtm180) REVERT: Z 72 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5853 (mtp85) REVERT: D 37 HIS cc_start: 0.6285 (OUTLIER) cc_final: 0.5572 (t-90) REVERT: E 46 LYS cc_start: 0.7955 (tttm) cc_final: 0.7363 (tppt) REVERT: p 36 ARG cc_start: 0.7650 (mmp80) cc_final: 0.6737 (tpp80) REVERT: p 84 LEU cc_start: 0.7833 (tp) cc_final: 0.7413 (tp) REVERT: p 149 VAL cc_start: 0.8135 (t) cc_final: 0.7631 (p) REVERT: p 150 MET cc_start: 0.7289 (mmm) cc_final: 0.7012 (mmm) REVERT: p 153 TYR cc_start: 0.7491 (m-80) cc_final: 0.6463 (m-80) REVERT: p 166 MET cc_start: 0.7546 (mmt) cc_final: 0.7017 (mmm) REVERT: p 225 ARG cc_start: 0.8824 (tmm-80) cc_final: 0.8037 (tpm170) REVERT: p 226 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7945 (mm-30) REVERT: q 4 MET cc_start: 0.7096 (mtm) cc_final: 0.6853 (mmt) REVERT: q 80 GLN cc_start: 0.8465 (tt0) cc_final: 0.7830 (tp40) REVERT: q 94 VAL cc_start: 0.7743 (m) cc_final: 0.7503 (t) REVERT: q 171 GLN cc_start: 0.8163 (pp30) cc_final: 0.7469 (pp30) REVERT: q 185 PRO cc_start: 0.8496 (Cg_endo) cc_final: 0.8282 (Cg_exo) REVERT: q 207 VAL cc_start: 0.7774 (t) cc_final: 0.7511 (t) REVERT: r 4 MET cc_start: 0.4231 (ptm) cc_final: 0.3478 (mmm) REVERT: r 26 LYS cc_start: 0.8803 (mptt) cc_final: 0.8323 (mmmt) REVERT: r 37 ARG cc_start: 0.5111 (mtm110) cc_final: 0.4335 (mtt-85) REVERT: r 60 ARG cc_start: 0.6814 (mmt180) cc_final: 0.6114 (ttt-90) REVERT: r 95 LEU cc_start: 0.8177 (tp) cc_final: 0.7443 (mp) REVERT: r 140 MET cc_start: 0.8135 (tmm) cc_final: 0.7815 (tmm) REVERT: r 163 GLU cc_start: 0.8535 (tt0) cc_final: 0.7659 (mp0) REVERT: r 164 GLU cc_start: 0.8102 (mp0) cc_final: 0.7736 (tm-30) REVERT: r 166 LYS cc_start: 0.7881 (mtpp) cc_final: 0.6951 (mmmt) REVERT: r 170 GLN cc_start: 0.8638 (mt0) cc_final: 0.8196 (mp10) REVERT: r 220 ARG cc_start: 0.7719 (mtm180) cc_final: 0.7295 (mtm180) REVERT: r 230 LEU cc_start: 0.7765 (tp) cc_final: 0.7443 (tp) REVERT: r 233 LYS cc_start: 0.8165 (tptm) cc_final: 0.7613 (ttmt) REVERT: r 294 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7288 (p) outliers start: 246 outliers final: 155 residues processed: 1512 average time/residue: 0.5954 time to fit residues: 1476.2140 Evaluate side-chains 1440 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1261 time to evaluate : 5.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 369 MET Chi-restraints excluded: chain J residue 388 ASN Chi-restraints excluded: chain J residue 404 ASP Chi-restraints excluded: chain J residue 414 VAL Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 580 GLU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 892 VAL Chi-restraints excluded: chain J residue 925 THR Chi-restraints excluded: chain J residue 942 PHE Chi-restraints excluded: chain J residue 952 LEU Chi-restraints excluded: chain J residue 979 PHE Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1046 MET Chi-restraints excluded: chain J residue 1048 LEU Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1064 VAL Chi-restraints excluded: chain J residue 1084 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1105 ASP Chi-restraints excluded: chain J residue 1172 CYS Chi-restraints excluded: chain J residue 1181 MET Chi-restraints excluded: chain J residue 1242 VAL Chi-restraints excluded: chain J residue 1327 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1328 THR Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 914 GLN Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1070 ASP Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1106 MET Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1159 ARG Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1174 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1234 SER Chi-restraints excluded: chain C residue 1262 CYS Chi-restraints excluded: chain C residue 1292 CYS Chi-restraints excluded: chain C residue 1327 THR Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain 5 residue 98 ASP Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 162 THR Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 5 residue 234 LEU Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 276 ASP Chi-restraints excluded: chain 5 residue 280 ASP Chi-restraints excluded: chain 6 residue 52 LEU Chi-restraints excluded: chain 6 residue 57 MET Chi-restraints excluded: chain 6 residue 151 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 242 CYS Chi-restraints excluded: chain 6 residue 246 ASP Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 4 residue 3 LEU Chi-restraints excluded: chain 4 residue 20 LEU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 55 GLU Chi-restraints excluded: chain 4 residue 76 VAL Chi-restraints excluded: chain 4 residue 159 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 72 ARG Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain p residue 169 LYS Chi-restraints excluded: chain p residue 183 GLN Chi-restraints excluded: chain p residue 202 ILE Chi-restraints excluded: chain p residue 205 LEU Chi-restraints excluded: chain p residue 245 THR Chi-restraints excluded: chain p residue 260 HIS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain q residue 229 MET Chi-restraints excluded: chain r residue 5 GLU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain r residue 114 LEU Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 244 GLU Chi-restraints excluded: chain r residue 273 VAL Chi-restraints excluded: chain r residue 294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 348 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 336 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 358 optimal weight: 10.0000 chunk 384 optimal weight: 0.7980 chunk 278 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 443 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 181 GLN ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 HIS ** A1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 422 ASN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 HIS ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1353 ASN ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 105 HIS 6 47 HIS 6 105 HIS 6 170 ASN ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 173 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 1.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 48092 Z= 0.164 Angle : 0.627 11.200 65374 Z= 0.306 Chirality : 0.040 0.299 7563 Planarity : 0.004 0.073 8405 Dihedral : 4.762 61.103 6509 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 3.14 % Allowed : 25.72 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.11), residues: 5871 helix: 0.32 (0.11), residues: 2438 sheet: -1.08 (0.20), residues: 629 loop : -0.87 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP p 117 HIS 0.011 0.001 HIS q 49 PHE 0.039 0.001 PHE q 177 TYR 0.027 0.001 TYR C 38 ARG 0.008 0.000 ARG 4 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1324 time to evaluate : 4.986 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: J 33 GLU cc_start: 0.8089 (mp0) cc_final: 0.7557 (mm-30) REVERT: J 84 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8139 (t0) REVERT: J 96 GLN cc_start: 0.8074 (mt0) cc_final: 0.7626 (mt0) REVERT: J 114 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7485 (mt) REVERT: J 125 ILE cc_start: 0.7802 (pt) cc_final: 0.7365 (pt) REVERT: J 217 GLN cc_start: 0.7716 (tp40) cc_final: 0.7308 (mt0) REVERT: J 310 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5916 (mm-30) REVERT: J 353 THR cc_start: 0.7983 (t) cc_final: 0.7723 (m) REVERT: J 382 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7898 (mptt) REVERT: J 388 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7898 (p0) REVERT: J 403 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7493 (mt-10) REVERT: J 404 ASP cc_start: 0.8736 (m-30) cc_final: 0.7708 (t0) REVERT: J 439 LYS cc_start: 0.8389 (pttt) cc_final: 0.7941 (tttm) REVERT: J 513 LYS cc_start: 0.8230 (ttmt) cc_final: 0.8002 (mtpt) REVERT: J 682 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7519 (mmt180) REVERT: J 737 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7421 (pt0) REVERT: J 815 PRO cc_start: 0.8292 (Cg_exo) cc_final: 0.8038 (Cg_endo) REVERT: J 900 ASP cc_start: 0.6388 (p0) cc_final: 0.6025 (p0) REVERT: J 911 ILE cc_start: 0.8201 (mt) cc_final: 0.7912 (mm) REVERT: J 979 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6433 (m-80) REVERT: J 1004 SER cc_start: 0.8219 (t) cc_final: 0.7877 (p) REVERT: J 1023 GLN cc_start: 0.7505 (mt0) cc_final: 0.7231 (mt0) REVERT: J 1046 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7154 (ptp) REVERT: J 1113 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7089 (mp) REVERT: J 1115 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7796 (mtp85) REVERT: J 1129 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7915 (ttm110) REVERT: J 1190 ASN cc_start: 0.8073 (t0) cc_final: 0.7639 (m110) REVERT: J 1206 ASP cc_start: 0.7644 (t0) cc_final: 0.7240 (t0) REVERT: J 1208 GLU cc_start: 0.8139 (tp30) cc_final: 0.7639 (pm20) REVERT: J 1229 HIS cc_start: 0.7011 (m-70) cc_final: 0.6321 (m-70) REVERT: J 1280 LYS cc_start: 0.8165 (tptt) cc_final: 0.7755 (tppt) REVERT: J 1351 PHE cc_start: 0.7950 (m-80) cc_final: 0.7361 (m-80) REVERT: A 35 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7078 (pt) REVERT: A 58 CYS cc_start: 0.8195 (p) cc_final: 0.7172 (m) REVERT: A 67 LEU cc_start: 0.8195 (mt) cc_final: 0.7564 (mp) REVERT: A 82 ASP cc_start: 0.7936 (m-30) cc_final: 0.7659 (m-30) REVERT: A 149 ASP cc_start: 0.7404 (t70) cc_final: 0.7088 (m-30) REVERT: A 157 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7368 (tpt) REVERT: A 160 VAL cc_start: 0.8085 (t) cc_final: 0.7836 (t) REVERT: A 232 ARG cc_start: 0.7845 (ttm170) cc_final: 0.6869 (mtt-85) REVERT: A 241 LYS cc_start: 0.8001 (ptmm) cc_final: 0.7775 (ttpt) REVERT: A 245 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.7684 (mtp85) REVERT: A 257 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7408 (p0) REVERT: A 281 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 295 THR cc_start: 0.7266 (p) cc_final: 0.6967 (p) REVERT: A 310 GLU cc_start: 0.7638 (mt-10) cc_final: 0.6666 (mm-30) REVERT: A 326 ASN cc_start: 0.7216 (t0) cc_final: 0.6789 (t0) REVERT: A 329 LYS cc_start: 0.6717 (ttpp) cc_final: 0.5740 (tptt) REVERT: A 336 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 360 ILE cc_start: 0.8615 (tp) cc_final: 0.8224 (tt) REVERT: A 374 ARG cc_start: 0.9083 (ptp90) cc_final: 0.8569 (ptp90) REVERT: A 382 LYS cc_start: 0.8394 (tptt) cc_final: 0.7014 (mptt) REVERT: A 397 VAL cc_start: 0.8251 (t) cc_final: 0.7998 (t) REVERT: A 405 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.6531 (mmt-90) REVERT: A 415 LYS cc_start: 0.9323 (tttp) cc_final: 0.8912 (ttmt) REVERT: A 701 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: A 739 LEU cc_start: 0.8099 (tp) cc_final: 0.7791 (tp) REVERT: A 807 LEU cc_start: 0.6849 (tp) cc_final: 0.6597 (tp) REVERT: A 856 MET cc_start: 0.8669 (tmm) cc_final: 0.7913 (ttp) REVERT: A 894 GLU cc_start: 0.6989 (tt0) cc_final: 0.6357 (tt0) REVERT: A 954 ASP cc_start: 0.7024 (m-30) cc_final: 0.6538 (t0) REVERT: A 958 ARG cc_start: 0.7237 (mtp180) cc_final: 0.7006 (mtp-110) REVERT: A 983 TYR cc_start: 0.8585 (m-80) cc_final: 0.8258 (m-80) REVERT: A 1041 THR cc_start: 0.8565 (m) cc_final: 0.7990 (p) REVERT: A 1069 ARG cc_start: 0.5959 (mtt90) cc_final: 0.5544 (mmt-90) REVERT: A 1098 TYR cc_start: 0.8275 (t80) cc_final: 0.7963 (t80) REVERT: A 1115 ARG cc_start: 0.6722 (mtm180) cc_final: 0.6505 (mtp85) REVERT: A 1119 MET cc_start: 0.7782 (mtt) cc_final: 0.7437 (mmt) REVERT: A 1207 THR cc_start: 0.7950 (m) cc_final: 0.7732 (p) REVERT: A 1267 ASN cc_start: 0.8518 (m-40) cc_final: 0.8264 (m-40) REVERT: A 1280 LYS cc_start: 0.6863 (mmtm) cc_final: 0.6419 (tttp) REVERT: A 1288 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7153 (mtm110) REVERT: A 1308 GLU cc_start: 0.6421 (mp0) cc_final: 0.5886 (mp0) REVERT: A 1320 GLU cc_start: 0.7684 (pp20) cc_final: 0.6918 (pp20) REVERT: A 1324 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7530 (pp) REVERT: A 1356 VAL cc_start: 0.7012 (t) cc_final: 0.6722 (t) REVERT: C 23 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7852 (m) REVERT: C 45 ARG cc_start: 0.6262 (ttp-170) cc_final: 0.6020 (ttp-110) REVERT: C 46 TYR cc_start: 0.5613 (m-80) cc_final: 0.4974 (m-80) REVERT: C 121 GLU cc_start: 0.7241 (tt0) cc_final: 0.6871 (mm-30) REVERT: C 137 THR cc_start: 0.8471 (t) cc_final: 0.8125 (p) REVERT: C 150 LYS cc_start: 0.6415 (mmtp) cc_final: 0.5925 (mmtp) REVERT: C 179 PHE cc_start: 0.7553 (t80) cc_final: 0.7345 (t80) REVERT: C 186 LYS cc_start: 0.7542 (ttpt) cc_final: 0.7316 (tttm) REVERT: C 276 THR cc_start: 0.7532 (m) cc_final: 0.7277 (p) REVERT: C 380 ASP cc_start: 0.8004 (t0) cc_final: 0.7446 (p0) REVERT: C 422 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6791 (t0) REVERT: C 453 VAL cc_start: 0.8788 (p) cc_final: 0.8461 (m) REVERT: C 477 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.7124 (ptp-110) REVERT: C 488 MET cc_start: 0.8752 (tpp) cc_final: 0.8310 (tpp) REVERT: C 598 LYS cc_start: 0.7168 (ttpp) cc_final: 0.6748 (tptm) REVERT: C 736 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6720 (mtp85) REVERT: C 909 ASP cc_start: 0.9404 (t70) cc_final: 0.8775 (p0) REVERT: C 919 ASN cc_start: 0.7356 (t0) cc_final: 0.6684 (m-40) REVERT: C 945 ASN cc_start: 0.7636 (t0) cc_final: 0.7313 (t0) REVERT: C 967 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.7958 (t70) REVERT: C 968 ARG cc_start: 0.7590 (ptm-80) cc_final: 0.6574 (ptt180) REVERT: C 1066 LYS cc_start: 0.8588 (ttpt) cc_final: 0.7786 (tptm) REVERT: C 1069 ARG cc_start: 0.6435 (mmm-85) cc_final: 0.6055 (mtp85) REVERT: C 1125 ASP cc_start: 0.8192 (t0) cc_final: 0.7899 (t0) REVERT: C 1129 ARG cc_start: 0.6947 (mmt-90) cc_final: 0.6523 (mpt180) REVERT: C 1159 ARG cc_start: 0.5784 (OUTLIER) cc_final: 0.5575 (ptt90) REVERT: C 1174 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5252 (mt) REVERT: C 1212 LYS cc_start: 0.7525 (mptt) cc_final: 0.7201 (ttmm) REVERT: C 1244 TYR cc_start: 0.8250 (m-80) cc_final: 0.7006 (m-80) REVERT: C 1268 THR cc_start: 0.8007 (t) cc_final: 0.7771 (p) REVERT: C 1348 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8519 (mm-30) REVERT: 5 25 GLN cc_start: 0.7814 (tt0) cc_final: 0.7399 (pt0) REVERT: 5 26 LYS cc_start: 0.6214 (mttm) cc_final: 0.5813 (mtmm) REVERT: 5 46 LEU cc_start: 0.7812 (mt) cc_final: 0.7557 (mp) REVERT: 5 89 ARG cc_start: 0.5702 (mtp85) cc_final: 0.5383 (mtp85) REVERT: 5 98 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6641 (p0) REVERT: 5 137 LYS cc_start: 0.6551 (mmtm) cc_final: 0.5955 (mmmm) REVERT: 5 175 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.7089 (ttp80) REVERT: 5 231 ARG cc_start: 0.7366 (mmp80) cc_final: 0.6468 (tpp80) REVERT: 5 237 LYS cc_start: 0.6799 (mttm) cc_final: 0.6545 (mmtp) REVERT: 5 269 GLU cc_start: 0.4025 (mt-10) cc_final: 0.3716 (mt-10) REVERT: 6 26 LYS cc_start: 0.7614 (mtmm) cc_final: 0.7072 (mtmm) REVERT: 6 36 LYS cc_start: 0.6929 (tptt) cc_final: 0.6379 (tppt) REVERT: 6 39 LYS cc_start: 0.6975 (ttpp) cc_final: 0.6605 (ptmt) REVERT: 6 182 LYS cc_start: 0.7638 (mtmm) cc_final: 0.6329 (mmpt) REVERT: 6 266 THR cc_start: 0.8140 (m) cc_final: 0.7734 (p) REVERT: 6 271 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6559 (tp) REVERT: 6 284 GLN cc_start: 0.7151 (pp30) cc_final: 0.6930 (pm20) REVERT: 4 51 VAL cc_start: 0.6911 (t) cc_final: 0.6215 (t) REVERT: 4 55 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: 4 57 MET cc_start: 0.6836 (ttt) cc_final: 0.6491 (tpp) REVERT: 4 165 GLN cc_start: 0.8254 (pt0) cc_final: 0.7563 (tm-30) REVERT: 4 233 LYS cc_start: 0.7248 (tptp) cc_final: 0.6664 (mmtp) REVERT: 4 241 MET cc_start: 0.5930 (mtm) cc_final: 0.5553 (mmt) REVERT: Z 49 ARG cc_start: 0.8103 (mmt90) cc_final: 0.7603 (mtm180) REVERT: D 37 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.5682 (t-90) REVERT: E 46 LYS cc_start: 0.7920 (tttm) cc_final: 0.7308 (tppt) REVERT: p 36 ARG cc_start: 0.7789 (mmp80) cc_final: 0.7385 (mmm-85) REVERT: p 84 LEU cc_start: 0.7979 (tp) cc_final: 0.7631 (tp) REVERT: p 150 MET cc_start: 0.7341 (mmm) cc_final: 0.7119 (mmm) REVERT: p 153 TYR cc_start: 0.7377 (m-80) cc_final: 0.6327 (m-80) REVERT: p 166 MET cc_start: 0.7526 (mmt) cc_final: 0.7236 (mmm) REVERT: p 225 ARG cc_start: 0.8816 (tmm-80) cc_final: 0.8143 (tpm170) REVERT: p 226 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7894 (mm-30) REVERT: q 73 MET cc_start: 0.7953 (ttp) cc_final: 0.7614 (ttm) REVERT: q 74 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5549 (ptm160) REVERT: q 80 GLN cc_start: 0.8313 (tt0) cc_final: 0.7952 (tp40) REVERT: q 171 GLN cc_start: 0.8200 (pp30) cc_final: 0.7559 (pp30) REVERT: q 185 PRO cc_start: 0.8330 (Cg_endo) cc_final: 0.8099 (Cg_exo) REVERT: q 207 VAL cc_start: 0.7741 (t) cc_final: 0.7476 (t) REVERT: q 218 TYR cc_start: 0.8311 (t80) cc_final: 0.7735 (t80) REVERT: q 231 LEU cc_start: 0.7912 (tp) cc_final: 0.7629 (tt) REVERT: q 239 MET cc_start: 0.7403 (tmm) cc_final: 0.7172 (tmm) REVERT: r 4 MET cc_start: 0.4162 (ptm) cc_final: 0.3464 (mmm) REVERT: r 26 LYS cc_start: 0.8695 (mptt) cc_final: 0.8236 (mmmt) REVERT: r 37 ARG cc_start: 0.5162 (mtm110) cc_final: 0.4459 (mtt-85) REVERT: r 60 ARG cc_start: 0.6676 (mmt180) cc_final: 0.6205 (ttt-90) REVERT: r 95 LEU cc_start: 0.8115 (tp) cc_final: 0.7433 (mp) REVERT: r 140 MET cc_start: 0.8129 (tmm) cc_final: 0.7740 (tmm) REVERT: r 163 GLU cc_start: 0.8597 (tt0) cc_final: 0.7850 (mp0) REVERT: r 164 GLU cc_start: 0.8078 (mp0) cc_final: 0.7731 (tm-30) REVERT: r 166 LYS cc_start: 0.7780 (mtpp) cc_final: 0.6827 (mmmt) REVERT: r 170 GLN cc_start: 0.8506 (mt0) cc_final: 0.7957 (mp10) REVERT: r 220 ARG cc_start: 0.7694 (mtm180) cc_final: 0.7222 (mtm180) REVERT: r 233 LYS cc_start: 0.8170 (tptm) cc_final: 0.7939 (tptm) REVERT: r 292 ASP cc_start: 0.6291 (p0) cc_final: 0.5976 (m-30) outliers start: 163 outliers final: 107 residues processed: 1420 average time/residue: 0.5935 time to fit residues: 1378.8990 Evaluate side-chains 1388 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1259 time to evaluate : 5.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 84 ASN Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 374 ARG Chi-restraints excluded: chain J residue 388 ASN Chi-restraints excluded: chain J residue 414 VAL Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 450 CYS Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 594 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 892 VAL Chi-restraints excluded: chain J residue 942 PHE Chi-restraints excluded: chain J residue 952 LEU Chi-restraints excluded: chain J residue 979 PHE Chi-restraints excluded: chain J residue 1046 MET Chi-restraints excluded: chain J residue 1048 LEU Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1064 VAL Chi-restraints excluded: chain J residue 1084 VAL Chi-restraints excluded: chain J residue 1105 ASP Chi-restraints excluded: chain J residue 1113 LEU Chi-restraints excluded: chain J residue 1172 CYS Chi-restraints excluded: chain J residue 1181 MET Chi-restraints excluded: chain J residue 1312 GLU Chi-restraints excluded: chain J residue 1327 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1328 THR Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 914 GLN Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1106 MET Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1159 ARG Chi-restraints excluded: chain C residue 1174 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1292 CYS Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 98 ASP Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain 5 residue 151 THR Chi-restraints excluded: chain 5 residue 159 LEU Chi-restraints excluded: chain 5 residue 162 THR Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 276 ASP Chi-restraints excluded: chain 6 residue 57 MET Chi-restraints excluded: chain 6 residue 242 CYS Chi-restraints excluded: chain 6 residue 246 ASP Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 55 GLU Chi-restraints excluded: chain 4 residue 76 VAL Chi-restraints excluded: chain 4 residue 159 LEU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain p residue 169 LYS Chi-restraints excluded: chain p residue 202 ILE Chi-restraints excluded: chain p residue 245 THR Chi-restraints excluded: chain p residue 260 HIS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 74 ARG Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain q residue 110 VAL Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 69 THR Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 273 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 512 optimal weight: 30.0000 chunk 540 optimal weight: 0.8980 chunk 492 optimal weight: 20.0000 chunk 525 optimal weight: 20.0000 chunk 316 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 412 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 474 optimal weight: 0.0980 chunk 496 optimal weight: 6.9990 chunk 523 optimal weight: 9.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 HIS ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN A 231 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 438 GLN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 HIS A1079 GLN A1133 HIS ** A1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS C 84 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 915 HIS C 965 HIS ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1217 HIS ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 47 HIS 6 105 HIS ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 173 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 1.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 48092 Z= 0.275 Angle : 0.701 10.447 65374 Z= 0.345 Chirality : 0.044 0.500 7563 Planarity : 0.005 0.093 8405 Dihedral : 4.950 63.659 6508 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 3.72 % Allowed : 25.32 % Favored : 70.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5871 helix: 0.08 (0.10), residues: 2467 sheet: -1.07 (0.20), residues: 639 loop : -0.91 (0.12), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP p 117 HIS 0.011 0.001 HIS A1133 PHE 0.038 0.002 PHE q 177 TYR 0.028 0.002 TYR C 38 ARG 0.012 0.001 ARG C 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1542 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1349 time to evaluate : 5.834 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: J 33 GLU cc_start: 0.8009 (mp0) cc_final: 0.7488 (mm-30) REVERT: J 82 ASP cc_start: 0.6816 (m-30) cc_final: 0.6585 (m-30) REVERT: J 84 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8466 (t0) REVERT: J 96 GLN cc_start: 0.8261 (mt0) cc_final: 0.7881 (mt0) REVERT: J 114 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7779 (mt) REVERT: J 125 ILE cc_start: 0.8014 (pt) cc_final: 0.7560 (pt) REVERT: J 217 GLN cc_start: 0.7977 (tp40) cc_final: 0.7497 (mt0) REVERT: J 237 ASP cc_start: 0.7391 (t0) cc_final: 0.7087 (p0) REVERT: J 242 PHE cc_start: 0.8195 (t80) cc_final: 0.7875 (t80) REVERT: J 310 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6148 (mm-30) REVERT: J 344 LEU cc_start: 0.6286 (tp) cc_final: 0.5567 (mt) REVERT: J 353 THR cc_start: 0.8217 (t) cc_final: 0.7968 (m) REVERT: J 382 LYS cc_start: 0.8533 (mmmm) cc_final: 0.7787 (mptt) REVERT: J 388 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8105 (p0) REVERT: J 403 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7745 (mt-10) REVERT: J 404 ASP cc_start: 0.8948 (m-30) cc_final: 0.8080 (t0) REVERT: J 439 LYS cc_start: 0.8488 (pttt) cc_final: 0.7806 (tttm) REVERT: J 737 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7724 (tp40) REVERT: J 774 THR cc_start: 0.6495 (m) cc_final: 0.6278 (t) REVERT: J 815 PRO cc_start: 0.8089 (Cg_exo) cc_final: 0.7880 (Cg_endo) REVERT: J 911 ILE cc_start: 0.8338 (mt) cc_final: 0.8110 (mm) REVERT: J 979 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: J 1004 SER cc_start: 0.8247 (t) cc_final: 0.7844 (p) REVERT: J 1023 GLN cc_start: 0.7578 (mt0) cc_final: 0.7327 (mt0) REVERT: J 1046 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7585 (ptp) REVERT: J 1088 LEU cc_start: 0.8306 (mt) cc_final: 0.8093 (mt) REVERT: J 1115 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7847 (mtp85) REVERT: J 1129 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7950 (ttm110) REVERT: J 1190 ASN cc_start: 0.8043 (t0) cc_final: 0.7515 (m110) REVERT: J 1206 ASP cc_start: 0.7777 (t0) cc_final: 0.7305 (t0) REVERT: J 1208 GLU cc_start: 0.8232 (tp30) cc_final: 0.7766 (pm20) REVERT: J 1247 ARG cc_start: 0.8457 (mmt-90) cc_final: 0.8021 (mmt-90) REVERT: J 1269 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8400 (mm-30) REVERT: J 1280 LYS cc_start: 0.8222 (tptt) cc_final: 0.7734 (tppt) REVERT: J 1351 PHE cc_start: 0.8068 (m-80) cc_final: 0.7658 (m-80) REVERT: A 31 MET cc_start: 0.6737 (ttt) cc_final: 0.6165 (ttp) REVERT: A 35 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7137 (pt) REVERT: A 58 CYS cc_start: 0.8342 (p) cc_final: 0.7242 (m) REVERT: A 67 LEU cc_start: 0.8603 (mt) cc_final: 0.7975 (mp) REVERT: A 82 ASP cc_start: 0.8105 (m-30) cc_final: 0.7816 (m-30) REVERT: A 127 ILE cc_start: 0.7635 (mt) cc_final: 0.7318 (tt) REVERT: A 149 ASP cc_start: 0.7198 (t70) cc_final: 0.6866 (m-30) REVERT: A 157 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7691 (tpp) REVERT: A 232 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7006 (mtt-85) REVERT: A 245 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7803 (mtp85) REVERT: A 257 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7229 (p0) REVERT: A 281 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7386 (tp40) REVERT: A 284 MET cc_start: 0.7601 (mmt) cc_final: 0.7204 (mmm) REVERT: A 329 LYS cc_start: 0.6816 (ttpp) cc_final: 0.5764 (tptm) REVERT: A 360 ILE cc_start: 0.8585 (tp) cc_final: 0.8259 (tt) REVERT: A 374 ARG cc_start: 0.9114 (ptp90) cc_final: 0.8708 (ptp90) REVERT: A 382 LYS cc_start: 0.8512 (tptt) cc_final: 0.7064 (mptt) REVERT: A 405 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.6695 (mmt180) REVERT: A 411 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7055 (pm20) REVERT: A 415 LYS cc_start: 0.9449 (tttp) cc_final: 0.9070 (ttmt) REVERT: A 416 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7873 (mt) REVERT: A 701 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: A 856 MET cc_start: 0.8848 (tmm) cc_final: 0.8178 (ttt) REVERT: A 874 GLN cc_start: 0.8178 (mp10) cc_final: 0.7716 (mp10) REVERT: A 894 GLU cc_start: 0.7631 (tt0) cc_final: 0.7132 (tt0) REVERT: A 903 GLN cc_start: 0.7620 (mt0) cc_final: 0.7124 (mt0) REVERT: A 919 ASN cc_start: 0.8605 (t0) cc_final: 0.8228 (t0) REVERT: A 954 ASP cc_start: 0.7323 (m-30) cc_final: 0.6709 (t0) REVERT: A 983 TYR cc_start: 0.8546 (m-80) cc_final: 0.8265 (m-80) REVERT: A 1015 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7472 (mt) REVERT: A 1041 THR cc_start: 0.8609 (m) cc_final: 0.8041 (p) REVERT: A 1069 ARG cc_start: 0.6120 (mtt90) cc_final: 0.5623 (mmt-90) REVERT: A 1088 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6384 (mt) REVERT: A 1098 TYR cc_start: 0.8071 (t80) cc_final: 0.7832 (t80) REVERT: A 1119 MET cc_start: 0.7783 (mtt) cc_final: 0.7576 (mmt) REVERT: A 1280 LYS cc_start: 0.7377 (mmtm) cc_final: 0.6851 (tttp) REVERT: A 1288 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7357 (mtm110) REVERT: A 1320 GLU cc_start: 0.7673 (pp20) cc_final: 0.6887 (pp20) REVERT: A 1324 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7540 (pp) REVERT: A 1356 VAL cc_start: 0.7323 (t) cc_final: 0.7031 (t) REVERT: C 46 TYR cc_start: 0.5953 (m-80) cc_final: 0.5696 (m-80) REVERT: C 68 THR cc_start: 0.8929 (m) cc_final: 0.8466 (p) REVERT: C 82 ASP cc_start: 0.8032 (t0) cc_final: 0.7242 (m-30) REVERT: C 137 THR cc_start: 0.8372 (t) cc_final: 0.8053 (p) REVERT: C 147 ILE cc_start: 0.8960 (tp) cc_final: 0.8353 (mm) REVERT: C 150 LYS cc_start: 0.6821 (mmtp) cc_final: 0.6393 (mmtp) REVERT: C 276 THR cc_start: 0.7877 (m) cc_final: 0.7413 (p) REVERT: C 284 MET cc_start: 0.7826 (mmp) cc_final: 0.7619 (mmp) REVERT: C 290 HIS cc_start: 0.7147 (m-70) cc_final: 0.6498 (m90) REVERT: C 380 ASP cc_start: 0.7822 (t0) cc_final: 0.7442 (p0) REVERT: C 415 LYS cc_start: 0.8553 (tttm) cc_final: 0.6533 (pttt) REVERT: C 437 VAL cc_start: 0.8393 (t) cc_final: 0.8134 (m) REVERT: C 453 VAL cc_start: 0.8821 (p) cc_final: 0.8483 (m) REVERT: C 526 ASN cc_start: 0.8176 (t0) cc_final: 0.6767 (t0) REVERT: C 736 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.6887 (mtp85) REVERT: C 909 ASP cc_start: 0.9424 (t70) cc_final: 0.8823 (p0) REVERT: C 919 ASN cc_start: 0.7606 (t0) cc_final: 0.6988 (m-40) REVERT: C 945 ASN cc_start: 0.7410 (t0) cc_final: 0.7115 (t0) REVERT: C 968 ARG cc_start: 0.7636 (ptm-80) cc_final: 0.7121 (ptp-170) REVERT: C 983 TYR cc_start: 0.7222 (m-80) cc_final: 0.6950 (m-80) REVERT: C 1069 ARG cc_start: 0.6700 (mmm-85) cc_final: 0.5883 (mtp180) REVERT: C 1129 ARG cc_start: 0.7101 (mmt-90) cc_final: 0.6579 (mpt180) REVERT: C 1159 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.5420 (ptt90) REVERT: C 1174 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5194 (mt) REVERT: C 1212 LYS cc_start: 0.7454 (mptt) cc_final: 0.7071 (ttmm) REVERT: C 1244 TYR cc_start: 0.8486 (m-80) cc_final: 0.7137 (m-80) REVERT: C 1247 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7864 (mmm160) REVERT: 5 25 GLN cc_start: 0.7496 (tt0) cc_final: 0.6966 (pt0) REVERT: 5 26 LYS cc_start: 0.6654 (mttm) cc_final: 0.6104 (mtmm) REVERT: 5 46 LEU cc_start: 0.7903 (mt) cc_final: 0.7689 (mp) REVERT: 5 68 PHE cc_start: 0.6740 (t80) cc_final: 0.6368 (t80) REVERT: 5 89 ARG cc_start: 0.5798 (mtp85) cc_final: 0.5454 (mtp85) REVERT: 5 98 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6698 (p0) REVERT: 5 137 LYS cc_start: 0.6169 (mmtm) cc_final: 0.5504 (mmmt) REVERT: 5 269 GLU cc_start: 0.5481 (mt-10) cc_final: 0.5238 (mt-10) REVERT: 6 26 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7104 (mtmm) REVERT: 6 36 LYS cc_start: 0.7056 (tptt) cc_final: 0.6521 (tppt) REVERT: 6 39 LYS cc_start: 0.7210 (ttpp) cc_final: 0.6809 (ptmt) REVERT: 6 178 MET cc_start: 0.6957 (pmm) cc_final: 0.6044 (pmm) REVERT: 6 182 LYS cc_start: 0.7583 (mtmm) cc_final: 0.6151 (mmpt) REVERT: 6 196 LEU cc_start: 0.8479 (tp) cc_final: 0.8266 (tt) REVERT: 6 240 ARG cc_start: 0.6600 (mtm110) cc_final: 0.6393 (ttp-110) REVERT: 6 255 LYS cc_start: 0.7367 (tttt) cc_final: 0.6856 (tppt) REVERT: 6 266 THR cc_start: 0.8212 (m) cc_final: 0.7832 (p) REVERT: 6 271 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6860 (tp) REVERT: 6 284 GLN cc_start: 0.7269 (pp30) cc_final: 0.6991 (pm20) REVERT: 4 19 PHE cc_start: 0.6415 (t80) cc_final: 0.6106 (t80) REVERT: 4 34 HIS cc_start: 0.7283 (m90) cc_final: 0.6729 (m90) REVERT: 4 51 VAL cc_start: 0.6971 (t) cc_final: 0.6206 (t) REVERT: 4 55 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: 4 218 GLU cc_start: 0.6421 (tm-30) cc_final: 0.5915 (mt-10) REVERT: 4 233 LYS cc_start: 0.7503 (tptp) cc_final: 0.6790 (mmtp) REVERT: 4 241 MET cc_start: 0.6297 (mtm) cc_final: 0.5899 (mmt) REVERT: Z 49 ARG cc_start: 0.8105 (mmt90) cc_final: 0.7600 (mtm180) REVERT: D 37 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5630 (t-90) REVERT: E 46 LYS cc_start: 0.8040 (tttm) cc_final: 0.7482 (tppt) REVERT: p 36 ARG cc_start: 0.7609 (mmp80) cc_final: 0.6924 (tpp80) REVERT: p 54 GLU cc_start: 0.6568 (pm20) cc_final: 0.5345 (tp30) REVERT: p 84 LEU cc_start: 0.7697 (tp) cc_final: 0.7319 (tp) REVERT: p 153 TYR cc_start: 0.7645 (m-80) cc_final: 0.6218 (m-80) REVERT: p 166 MET cc_start: 0.7842 (mmt) cc_final: 0.7315 (mmm) REVERT: p 225 ARG cc_start: 0.8817 (tmm-80) cc_final: 0.8138 (tpm170) REVERT: p 226 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8035 (mm-30) REVERT: q 20 ASP cc_start: 0.6910 (m-30) cc_final: 0.6583 (m-30) REVERT: q 74 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.5418 (ptm160) REVERT: q 80 GLN cc_start: 0.8206 (tt0) cc_final: 0.7961 (tp40) REVERT: q 156 PHE cc_start: 0.6044 (t80) cc_final: 0.5558 (t80) REVERT: q 171 GLN cc_start: 0.8479 (pp30) cc_final: 0.7943 (pp30) REVERT: q 207 VAL cc_start: 0.7835 (t) cc_final: 0.7580 (t) REVERT: q 239 MET cc_start: 0.7659 (tmm) cc_final: 0.7363 (tmm) REVERT: r 4 MET cc_start: 0.4326 (ptm) cc_final: 0.3508 (mmm) REVERT: r 26 LYS cc_start: 0.8679 (mptt) cc_final: 0.8388 (mmpt) REVERT: r 60 ARG cc_start: 0.6863 (mmt180) cc_final: 0.6321 (ttt-90) REVERT: r 95 LEU cc_start: 0.8159 (tp) cc_final: 0.7453 (mp) REVERT: r 131 GLU cc_start: 0.8313 (pt0) cc_final: 0.7615 (mm-30) REVERT: r 140 MET cc_start: 0.8243 (tmm) cc_final: 0.7860 (tmm) REVERT: r 163 GLU cc_start: 0.8492 (tt0) cc_final: 0.7944 (mp0) REVERT: r 166 LYS cc_start: 0.7953 (mtpp) cc_final: 0.7038 (mmmt) REVERT: r 170 GLN cc_start: 0.8515 (mt0) cc_final: 0.8142 (mp10) REVERT: r 175 ILE cc_start: 0.7866 (tp) cc_final: 0.7574 (tp) REVERT: r 220 ARG cc_start: 0.7820 (mtm180) cc_final: 0.7546 (mtm180) REVERT: r 225 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6268 (mm-30) REVERT: r 233 LYS cc_start: 0.8249 (tptm) cc_final: 0.7824 (tttm) REVERT: r 292 ASP cc_start: 0.6246 (p0) cc_final: 0.5831 (m-30) outliers start: 193 outliers final: 136 residues processed: 1467 average time/residue: 0.6048 time to fit residues: 1450.4031 Evaluate side-chains 1432 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1274 time to evaluate : 5.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 84 ASN Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 374 ARG Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 388 ASN Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 450 CYS Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 580 GLU Chi-restraints excluded: chain J residue 599 THR Chi-restraints excluded: chain J residue 704 SER Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 892 VAL Chi-restraints excluded: chain J residue 925 THR Chi-restraints excluded: chain J residue 942 PHE Chi-restraints excluded: chain J residue 952 LEU Chi-restraints excluded: chain J residue 979 PHE Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1046 MET Chi-restraints excluded: chain J residue 1048 LEU Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1064 VAL Chi-restraints excluded: chain J residue 1084 VAL Chi-restraints excluded: chain J residue 1105 ASP Chi-restraints excluded: chain J residue 1172 CYS Chi-restraints excluded: chain J residue 1242 VAL Chi-restraints excluded: chain J residue 1291 ASP Chi-restraints excluded: chain J residue 1302 VAL Chi-restraints excluded: chain J residue 1312 GLU Chi-restraints excluded: chain J residue 1327 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1328 THR Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 914 GLN Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1159 ARG Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1174 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1292 CYS Chi-restraints excluded: chain C residue 1324 ILE Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 98 ASP Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain 5 residue 151 THR Chi-restraints excluded: chain 5 residue 162 THR Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 276 ASP Chi-restraints excluded: chain 6 residue 242 CYS Chi-restraints excluded: chain 6 residue 246 ASP Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 55 GLU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain p residue 194 ASP Chi-restraints excluded: chain p residue 245 THR Chi-restraints excluded: chain p residue 260 HIS Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 74 ARG Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 114 LEU Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 225 GLU Chi-restraints excluded: chain r residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 345 optimal weight: 5.9990 chunk 555 optimal weight: 30.0000 chunk 339 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 386 optimal weight: 8.9990 chunk 582 optimal weight: 8.9990 chunk 536 optimal weight: 6.9990 chunk 464 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 358 optimal weight: 3.9990 chunk 284 optimal weight: 0.2980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 290 HIS ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 969 HIS A 231 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 HIS A1133 HIS A1248 HIS C 81 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 47 HIS 6 105 HIS ** 6 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 54 ASN ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 212 ASN ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 148 GLN q 192 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 1.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 48092 Z= 0.189 Angle : 0.668 14.108 65374 Z= 0.324 Chirality : 0.042 0.332 7563 Planarity : 0.005 0.076 8405 Dihedral : 4.833 61.561 6508 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 3.03 % Allowed : 26.63 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.11), residues: 5871 helix: 0.25 (0.11), residues: 2437 sheet: -1.06 (0.20), residues: 658 loop : -0.86 (0.12), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP p 117 HIS 0.014 0.001 HIS 6 158 PHE 0.043 0.001 PHE q 177 TYR 0.028 0.001 TYR A 994 ARG 0.010 0.000 ARG A 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11742 Ramachandran restraints generated. 5871 Oldfield, 0 Emsley, 5871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1466 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1309 time to evaluate : 5.510 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: J 33 GLU cc_start: 0.8001 (mp0) cc_final: 0.7504 (mm-30) REVERT: J 84 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8491 (t0) REVERT: J 96 GLN cc_start: 0.8183 (mt0) cc_final: 0.7743 (mt0) REVERT: J 114 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7623 (mt) REVERT: J 125 ILE cc_start: 0.7995 (pt) cc_final: 0.7570 (pt) REVERT: J 217 GLN cc_start: 0.7927 (tp40) cc_final: 0.7481 (mt0) REVERT: J 310 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6134 (mm-30) REVERT: J 344 LEU cc_start: 0.6195 (tp) cc_final: 0.5616 (mt) REVERT: J 352 LEU cc_start: 0.7815 (mt) cc_final: 0.7285 (mt) REVERT: J 353 THR cc_start: 0.8267 (t) cc_final: 0.8000 (m) REVERT: J 382 LYS cc_start: 0.8519 (mmmm) cc_final: 0.7799 (mptt) REVERT: J 388 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.8041 (p0) REVERT: J 403 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7752 (mt-10) REVERT: J 404 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.7790 (t0) REVERT: J 439 LYS cc_start: 0.8277 (pttt) cc_final: 0.7826 (tttm) REVERT: J 737 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7670 (tp40) REVERT: J 774 THR cc_start: 0.6459 (m) cc_final: 0.6246 (t) REVERT: J 810 ASP cc_start: 0.7528 (t0) cc_final: 0.7280 (t0) REVERT: J 815 PRO cc_start: 0.8078 (Cg_exo) cc_final: 0.7871 (Cg_endo) REVERT: J 911 ILE cc_start: 0.8359 (mt) cc_final: 0.8121 (mm) REVERT: J 979 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: J 1004 SER cc_start: 0.8204 (t) cc_final: 0.7712 (m) REVERT: J 1046 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7593 (ptp) REVERT: J 1113 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7151 (mp) REVERT: J 1129 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7959 (ttm110) REVERT: J 1190 ASN cc_start: 0.8036 (t0) cc_final: 0.7574 (m110) REVERT: J 1206 ASP cc_start: 0.7733 (t0) cc_final: 0.7201 (t0) REVERT: J 1280 LYS cc_start: 0.8242 (tptt) cc_final: 0.7832 (tppt) REVERT: A 31 MET cc_start: 0.6654 (ttt) cc_final: 0.6034 (ttp) REVERT: A 35 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7122 (pt) REVERT: A 67 LEU cc_start: 0.8602 (mt) cc_final: 0.8006 (mp) REVERT: A 82 ASP cc_start: 0.8205 (m-30) cc_final: 0.7961 (m-30) REVERT: A 127 ILE cc_start: 0.7642 (mt) cc_final: 0.7335 (tt) REVERT: A 149 ASP cc_start: 0.7194 (t70) cc_final: 0.6852 (m-30) REVERT: A 157 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7685 (tpp) REVERT: A 232 ARG cc_start: 0.7352 (ttm170) cc_final: 0.6722 (mtt-85) REVERT: A 257 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7146 (p0) REVERT: A 281 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7448 (tp40) REVERT: A 329 LYS cc_start: 0.6924 (ttpp) cc_final: 0.5723 (tptp) REVERT: A 360 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8307 (tt) REVERT: A 374 ARG cc_start: 0.8954 (ptp90) cc_final: 0.8546 (ptp90) REVERT: A 382 LYS cc_start: 0.8504 (tptt) cc_final: 0.6851 (mptt) REVERT: A 405 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.6683 (mmt180) REVERT: A 411 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7025 (pm20) REVERT: A 416 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7692 (mt) REVERT: A 444 ASP cc_start: 0.8247 (m-30) cc_final: 0.7999 (t0) REVERT: A 701 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: A 856 MET cc_start: 0.8695 (tmm) cc_final: 0.8219 (ttt) REVERT: A 894 GLU cc_start: 0.7159 (tt0) cc_final: 0.6816 (tt0) REVERT: A 903 GLN cc_start: 0.7696 (mt0) cc_final: 0.7186 (mt0) REVERT: A 919 ASN cc_start: 0.8748 (t0) cc_final: 0.8412 (t0) REVERT: A 954 ASP cc_start: 0.7276 (m-30) cc_final: 0.6696 (t0) REVERT: A 983 TYR cc_start: 0.8552 (m-80) cc_final: 0.8333 (m-80) REVERT: A 1015 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 1041 THR cc_start: 0.8700 (m) cc_final: 0.8104 (p) REVERT: A 1069 ARG cc_start: 0.6164 (mtt90) cc_final: 0.5632 (mmt-90) REVERT: A 1086 MET cc_start: 0.7961 (mpp) cc_final: 0.7722 (mpp) REVERT: A 1088 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5912 (mt) REVERT: A 1098 TYR cc_start: 0.8054 (t80) cc_final: 0.7829 (t80) REVERT: A 1111 GLN cc_start: 0.7591 (pm20) cc_final: 0.6404 (mt0) REVERT: A 1119 MET cc_start: 0.7899 (mtt) cc_final: 0.7633 (mmt) REVERT: A 1280 LYS cc_start: 0.7358 (mmtm) cc_final: 0.6843 (tttp) REVERT: A 1288 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7371 (mtm110) REVERT: A 1320 GLU cc_start: 0.7697 (pp20) cc_final: 0.6916 (pp20) REVERT: A 1324 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7585 (pp) REVERT: A 1356 VAL cc_start: 0.7293 (t) cc_final: 0.7010 (t) REVERT: C 23 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8287 (m) REVERT: C 45 ARG cc_start: 0.6552 (ttp-170) cc_final: 0.6170 (ttp-110) REVERT: C 46 TYR cc_start: 0.5929 (m-80) cc_final: 0.5523 (m-80) REVERT: C 82 ASP cc_start: 0.8048 (t0) cc_final: 0.7286 (m-30) REVERT: C 137 THR cc_start: 0.8322 (t) cc_final: 0.8058 (p) REVERT: C 147 ILE cc_start: 0.9089 (tp) cc_final: 0.8470 (mm) REVERT: C 150 LYS cc_start: 0.6744 (mmtp) cc_final: 0.6179 (mmtp) REVERT: C 179 PHE cc_start: 0.7887 (t80) cc_final: 0.7558 (t80) REVERT: C 240 LEU cc_start: 0.8328 (tp) cc_final: 0.7960 (tt) REVERT: C 276 THR cc_start: 0.7810 (m) cc_final: 0.7408 (p) REVERT: C 380 ASP cc_start: 0.7880 (t0) cc_final: 0.7466 (p0) REVERT: C 415 LYS cc_start: 0.8599 (tttm) cc_final: 0.6562 (pttt) REVERT: C 437 VAL cc_start: 0.8363 (t) cc_final: 0.8092 (m) REVERT: C 453 VAL cc_start: 0.8847 (p) cc_final: 0.8500 (m) REVERT: C 736 ARG cc_start: 0.7244 (mtm-85) cc_final: 0.6688 (mtp85) REVERT: C 909 ASP cc_start: 0.9457 (t70) cc_final: 0.8860 (p0) REVERT: C 919 ASN cc_start: 0.7492 (t0) cc_final: 0.6993 (m-40) REVERT: C 945 ASN cc_start: 0.7430 (t0) cc_final: 0.7149 (t0) REVERT: C 958 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7728 (ttm110) REVERT: C 967 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8257 (t70) REVERT: C 968 ARG cc_start: 0.7584 (ptm-80) cc_final: 0.7086 (ptp-170) REVERT: C 983 TYR cc_start: 0.7566 (m-80) cc_final: 0.6705 (m-80) REVERT: C 1066 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7616 (tptm) REVERT: C 1069 ARG cc_start: 0.6752 (mmm-85) cc_final: 0.5923 (mtp180) REVERT: C 1129 ARG cc_start: 0.7043 (mmt-90) cc_final: 0.6556 (mpt180) REVERT: C 1159 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5462 (ptt90) REVERT: C 1174 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5650 (mt) REVERT: C 1212 LYS cc_start: 0.7517 (mptt) cc_final: 0.6955 (ttmm) REVERT: C 1244 TYR cc_start: 0.8470 (m-80) cc_final: 0.7035 (m-80) REVERT: C 1247 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7996 (mmm160) REVERT: 5 25 GLN cc_start: 0.7423 (tt0) cc_final: 0.6921 (pt0) REVERT: 5 26 LYS cc_start: 0.6610 (mttm) cc_final: 0.6072 (mtmm) REVERT: 5 98 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6676 (p0) REVERT: 5 231 ARG cc_start: 0.7403 (mmp80) cc_final: 0.5938 (mmt-90) REVERT: 5 269 GLU cc_start: 0.5526 (mt-10) cc_final: 0.5255 (mt-10) REVERT: 5 278 TYR cc_start: 0.8454 (p90) cc_final: 0.7880 (p90) REVERT: 6 26 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7385 (mtmm) REVERT: 6 36 LYS cc_start: 0.6748 (tptt) cc_final: 0.6202 (tppt) REVERT: 6 39 LYS cc_start: 0.7133 (ttpp) cc_final: 0.6672 (ptmt) REVERT: 6 99 ARG cc_start: 0.7449 (mtm180) cc_final: 0.7208 (mtm110) REVERT: 6 182 LYS cc_start: 0.7586 (mtmm) cc_final: 0.6152 (mmpt) REVERT: 6 191 HIS cc_start: 0.8042 (t70) cc_final: 0.7457 (t70) REVERT: 6 196 LEU cc_start: 0.8499 (tp) cc_final: 0.8298 (tt) REVERT: 6 255 LYS cc_start: 0.7356 (tttt) cc_final: 0.6860 (tppt) REVERT: 6 271 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6969 (tp) REVERT: 6 273 GLU cc_start: 0.6953 (tp30) cc_final: 0.6054 (tt0) REVERT: 6 284 GLN cc_start: 0.7200 (pp30) cc_final: 0.6909 (pm20) REVERT: 4 19 PHE cc_start: 0.6427 (t80) cc_final: 0.6102 (t80) REVERT: 4 28 ASP cc_start: 0.6770 (m-30) cc_final: 0.6211 (m-30) REVERT: 4 34 HIS cc_start: 0.7281 (m90) cc_final: 0.6779 (m90) REVERT: 4 51 VAL cc_start: 0.7050 (t) cc_final: 0.6172 (t) REVERT: 4 55 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: 4 165 GLN cc_start: 0.8310 (pt0) cc_final: 0.7585 (tm-30) REVERT: 4 233 LYS cc_start: 0.7757 (tptp) cc_final: 0.6898 (mmtp) REVERT: Z 49 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7566 (mtm180) REVERT: D 37 HIS cc_start: 0.6750 (OUTLIER) cc_final: 0.5821 (t-90) REVERT: E 46 LYS cc_start: 0.8006 (tttm) cc_final: 0.7768 (tppt) REVERT: p 36 ARG cc_start: 0.7717 (mmp80) cc_final: 0.6943 (tpp80) REVERT: p 54 GLU cc_start: 0.6633 (pm20) cc_final: 0.5481 (tp30) REVERT: p 84 LEU cc_start: 0.7621 (tp) cc_final: 0.7315 (tp) REVERT: p 153 TYR cc_start: 0.7551 (m-80) cc_final: 0.6145 (m-80) REVERT: p 166 MET cc_start: 0.7838 (mmt) cc_final: 0.7500 (mmm) REVERT: p 225 ARG cc_start: 0.8834 (tmm-80) cc_final: 0.8156 (tpm170) REVERT: p 226 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8064 (mm-30) REVERT: q 20 ASP cc_start: 0.6956 (m-30) cc_final: 0.6601 (m-30) REVERT: q 74 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5575 (ptm160) REVERT: q 156 PHE cc_start: 0.6084 (t80) cc_final: 0.5617 (t80) REVERT: q 171 GLN cc_start: 0.8405 (pp30) cc_final: 0.7906 (pp30) REVERT: q 207 VAL cc_start: 0.7753 (t) cc_final: 0.7488 (t) REVERT: q 231 LEU cc_start: 0.8046 (tp) cc_final: 0.7702 (tt) REVERT: q 239 MET cc_start: 0.7580 (tmm) cc_final: 0.7272 (tmm) REVERT: r 4 MET cc_start: 0.4303 (ptm) cc_final: 0.3468 (mmm) REVERT: r 26 LYS cc_start: 0.8599 (mptt) cc_final: 0.8178 (mmmt) REVERT: r 37 ARG cc_start: 0.5565 (mtm180) cc_final: 0.4738 (mtt-85) REVERT: r 60 ARG cc_start: 0.6801 (mmt180) cc_final: 0.6267 (ttt-90) REVERT: r 95 LEU cc_start: 0.8053 (tp) cc_final: 0.7736 (mp) REVERT: r 140 MET cc_start: 0.8249 (tmm) cc_final: 0.7870 (tmm) REVERT: r 155 LEU cc_start: 0.7280 (mm) cc_final: 0.6739 (mm) REVERT: r 163 GLU cc_start: 0.8892 (tt0) cc_final: 0.8207 (mp0) REVERT: r 166 LYS cc_start: 0.7859 (mtpp) cc_final: 0.6882 (mmmt) REVERT: r 170 GLN cc_start: 0.8449 (mt0) cc_final: 0.7947 (mp10) REVERT: r 220 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7505 (mtm180) REVERT: r 233 LYS cc_start: 0.8213 (tptm) cc_final: 0.7897 (tttm) REVERT: r 292 ASP cc_start: 0.6196 (p0) cc_final: 0.5800 (m-30) outliers start: 157 outliers final: 110 residues processed: 1398 average time/residue: 0.6081 time to fit residues: 1383.0703 Evaluate side-chains 1394 residues out of total 5189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1258 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 84 ASN Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 310 GLU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 374 ARG Chi-restraints excluded: chain J residue 388 ASN Chi-restraints excluded: chain J residue 404 ASP Chi-restraints excluded: chain J residue 450 CYS Chi-restraints excluded: chain J residue 545 ASN Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 594 LEU Chi-restraints excluded: chain J residue 704 SER Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 892 VAL Chi-restraints excluded: chain J residue 925 THR Chi-restraints excluded: chain J residue 942 PHE Chi-restraints excluded: chain J residue 979 PHE Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1046 MET Chi-restraints excluded: chain J residue 1048 LEU Chi-restraints excluded: chain J residue 1057 VAL Chi-restraints excluded: chain J residue 1064 VAL Chi-restraints excluded: chain J residue 1105 ASP Chi-restraints excluded: chain J residue 1113 LEU Chi-restraints excluded: chain J residue 1172 CYS Chi-restraints excluded: chain J residue 1242 VAL Chi-restraints excluded: chain J residue 1312 GLU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1328 THR Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 855 GLU Chi-restraints excluded: chain C residue 861 VAL Chi-restraints excluded: chain C residue 914 GLN Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain C residue 1094 THR Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1152 THR Chi-restraints excluded: chain C residue 1159 ARG Chi-restraints excluded: chain C residue 1165 VAL Chi-restraints excluded: chain C residue 1174 LEU Chi-restraints excluded: chain C residue 1199 MET Chi-restraints excluded: chain C residue 1292 CYS Chi-restraints excluded: chain C residue 1324 ILE Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 98 ASP Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain 5 residue 151 THR Chi-restraints excluded: chain 5 residue 162 THR Chi-restraints excluded: chain 5 residue 187 ASN Chi-restraints excluded: chain 5 residue 246 ASP Chi-restraints excluded: chain 5 residue 276 ASP Chi-restraints excluded: chain 6 residue 57 MET Chi-restraints excluded: chain 6 residue 242 CYS Chi-restraints excluded: chain 6 residue 246 ASP Chi-restraints excluded: chain 6 residue 268 LEU Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 55 GLU Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain p residue 245 THR Chi-restraints excluded: chain p residue 260 HIS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 74 ARG Chi-restraints excluded: chain q residue 85 VAL Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain q residue 202 LEU Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 368 optimal weight: 20.0000 chunk 494 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 427 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 464 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 477 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 290 HIS ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 969 HIS A 231 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 731 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN A1133 HIS ** A1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 70 ASN 6 18 ASN 6 47 HIS 6 105 HIS 6 158 HIS ** 4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 212 ASN ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 173 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.154300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.136974 restraints weight = 67470.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.139297 restraints weight = 38642.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.140820 restraints weight = 25701.722| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 1.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 48092 Z= 0.253 Angle : 0.747 59.167 65374 Z= 0.386 Chirality : 0.042 0.332 7563 Planarity : 0.005 0.077 8405 Dihedral : 4.829 61.551 6508 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 3.07 % Allowed : 26.76 % Favored : 70.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.11), residues: 5871 helix: 0.25 (0.11), residues: 2437 sheet: -1.06 (0.20), residues: 658 loop : -0.86 (0.12), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP p 117 HIS 0.010 0.001 HIS 6 158 PHE 0.041 0.001 PHE q 177 TYR 0.060 0.001 TYR C1215 ARG 0.008 0.000 ARG J1294 =============================================================================== Job complete usr+sys time: 18847.18 seconds wall clock time: 333 minutes 3.85 seconds (19983.85 seconds total)