Starting phenix.real_space_refine on Thu Feb 22 06:49:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7faf_31503/02_2024/7faf_31503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7faf_31503/02_2024/7faf_31503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7faf_31503/02_2024/7faf_31503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7faf_31503/02_2024/7faf_31503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7faf_31503/02_2024/7faf_31503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7faf_31503/02_2024/7faf_31503.pdb" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 144 5.16 5 C 21140 2.51 5 N 5558 2.21 5 O 6446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 122": "NH1" <-> "NH2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "L ARG 127": "NH1" <-> "NH2" Residue "L GLU 180": "OE1" <-> "OE2" Residue "L GLU 206": "OE1" <-> "OE2" Residue "L ARG 230": "NH1" <-> "NH2" Residue "c ARG 127": "NH1" <-> "NH2" Residue "c GLU 180": "OE1" <-> "OE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "c ARG 230": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "d ARG 122": "NH1" <-> "NH2" Residue "f ARG 127": "NH1" <-> "NH2" Residue "f GLU 180": "OE1" <-> "OE2" Residue "f GLU 206": "OE1" <-> "OE2" Residue "f ARG 230": "NH1" <-> "NH2" Residue "g ARG 121": "NH1" <-> "NH2" Residue "g ARG 122": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C ARG 1107": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33288 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7767 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 52, 'TRANS': 943} Chain breaks: 9 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "c" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "d" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "f" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "g" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "B" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 53, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7743 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 941} Chain breaks: 10 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 16.58, per 1000 atoms: 0.50 Number of scatterers: 33288 At special positions: 0 Unit cell: (220.19, 184.3, 182.36, 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 144 16.00 O 6446 8.00 N 5558 7.00 C 21140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.02 Simple disulfide: pdb=" SG CYS H 168 " - pdb=" SG CYS H 224 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.04 Simple disulfide: pdb=" SG CYS L 153 " - pdb=" SG CYS L 213 " distance=2.04 Simple disulfide: pdb=" SG CYS c 42 " - pdb=" SG CYS c 107 " distance=2.04 Simple disulfide: pdb=" SG CYS c 153 " - pdb=" SG CYS c 213 " distance=2.04 Simple disulfide: pdb=" SG CYS d 41 " - pdb=" SG CYS d 115 " distance=2.02 Simple disulfide: pdb=" SG CYS d 168 " - pdb=" SG CYS d 224 " distance=2.03 Simple disulfide: pdb=" SG CYS f 42 " - pdb=" SG CYS f 107 " distance=2.04 Simple disulfide: pdb=" SG CYS f 153 " - pdb=" SG CYS f 213 " distance=2.04 Simple disulfide: pdb=" SG CYS g 41 " - pdb=" SG CYS g 115 " distance=2.02 Simple disulfide: pdb=" SG CYS g 168 " - pdb=" SG CYS g 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.99 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.07 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.94 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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: 13.38 Conformation dependent library (CDL) restraints added in 6.3 seconds 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 73 sheets defined 20.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.566A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.830A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.654A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.665A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.766A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.527A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.511A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.929A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.726A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 965 removed outlier: 4.092A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.417A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.684A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 155 through 159 removed outlier: 3.565A pdb=" N THR H 159 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 229 through 232 Processing helix chain 'L' and resid 98 through 102 Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.749A pdb=" N GLU L 206 " --> pdb=" O LYS L 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 202 through 206' Processing helix chain 'c' and resid 98 through 102 Processing helix chain 'c' and resid 140 through 145 Processing helix chain 'c' and resid 202 through 206 removed outlier: 3.749A pdb=" N GLU c 206 " --> pdb=" O LYS c 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 202 through 206' Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 155 through 159 removed outlier: 3.564A pdb=" N THR d 159 " --> pdb=" O SER d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 215 through 217 No H-bonds generated for 'chain 'd' and resid 215 through 217' Processing helix chain 'd' and resid 229 through 232 Processing helix chain 'f' and resid 98 through 102 Processing helix chain 'f' and resid 140 through 145 Processing helix chain 'f' and resid 202 through 206 removed outlier: 3.749A pdb=" N GLU f 206 " --> pdb=" O LYS f 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 202 through 206' Processing helix chain 'g' and resid 106 through 110 Processing helix chain 'g' and resid 155 through 159 removed outlier: 3.565A pdb=" N THR g 159 " --> pdb=" O SER g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 215 through 217 No H-bonds generated for 'chain 'g' and resid 215 through 217' Processing helix chain 'g' and resid 229 through 232 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.495A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.549A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.914A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.611A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.880A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.134A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.553A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.569A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 980 removed outlier: 3.640A pdb=" N ILE B 980 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.400A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.683A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.757A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.132A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.964A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 410' Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 568 through 572 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.666A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.766A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 806 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.574A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.527A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.511A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.503A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.929A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.601A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.566A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.531A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.685A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.041A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.720A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.775A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.433A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.883A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.566A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.880A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.534A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.248A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.248A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.518A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AB6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.876A pdb=" N GLU H 29 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 148 through 152 removed outlier: 3.658A pdb=" N SER H 208 " --> pdb=" O CYS H 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR H 204 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 148 through 152 removed outlier: 3.658A pdb=" N SER H 208 " --> pdb=" O CYS H 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR H 204 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER H 205 " --> pdb=" O VAL H 197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.781A pdb=" N CYS H 224 " --> pdb=" O LYS H 237 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 237 " --> pdb=" O CYS H 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 23 through 26 removed outlier: 3.645A pdb=" N THR L 91 " --> pdb=" O SER L 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 72 through 73 removed outlier: 6.381A pdb=" N TRP L 54 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR L 68 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU L 52 " --> pdb=" O TYR L 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 133 through 137 removed outlier: 5.625A pdb=" N TYR L 192 " --> pdb=" O ASN L 157 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 173 through 174 removed outlier: 4.707A pdb=" N TRP L 167 " --> pdb=" O GLN L 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 23 through 26 removed outlier: 3.644A pdb=" N THR c 91 " --> pdb=" O SER c 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 72 through 73 removed outlier: 6.381A pdb=" N TRP c 54 " --> pdb=" O LEU c 66 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR c 68 " --> pdb=" O LEU c 52 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU c 52 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 133 through 137 removed outlier: 5.625A pdb=" N TYR c 192 " --> pdb=" O ASN c 157 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 173 through 174 removed outlier: 4.708A pdb=" N TRP c 167 " --> pdb=" O GLN c 174 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 22 through 25 Processing sheet with id=AD1, first strand: chain 'd' and resid 29 through 31 removed outlier: 6.876A pdb=" N GLU d 29 " --> pdb=" O THR d 138 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG d 57 " --> pdb=" O TRP d 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP d 66 " --> pdb=" O ARG d 57 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 148 through 152 removed outlier: 3.660A pdb=" N SER d 208 " --> pdb=" O CYS d 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR d 204 " --> pdb=" O ASP d 172 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 148 through 152 removed outlier: 3.660A pdb=" N SER d 208 " --> pdb=" O CYS d 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR d 204 " --> pdb=" O ASP d 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER d 205 " --> pdb=" O VAL d 197 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 179 through 182 removed outlier: 3.780A pdb=" N CYS d 224 " --> pdb=" O LYS d 237 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS d 237 " --> pdb=" O CYS d 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'f' and resid 23 through 26 removed outlier: 3.644A pdb=" N THR f 91 " --> pdb=" O SER f 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 72 through 73 removed outlier: 6.380A pdb=" N TRP f 54 " --> pdb=" O LEU f 66 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR f 68 " --> pdb=" O LEU f 52 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU f 52 " --> pdb=" O TYR f 68 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 133 through 137 removed outlier: 5.625A pdb=" N TYR f 192 " --> pdb=" O ASN f 157 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 173 through 174 removed outlier: 4.708A pdb=" N TRP f 167 " --> pdb=" O GLN f 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 22 through 25 Processing sheet with id=AE1, first strand: chain 'g' and resid 29 through 31 removed outlier: 6.876A pdb=" N GLU g 29 " --> pdb=" O THR g 138 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG g 57 " --> pdb=" O TRP g 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP g 66 " --> pdb=" O ARG g 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 148 through 152 removed outlier: 3.658A pdb=" N SER g 208 " --> pdb=" O CYS g 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR g 204 " --> pdb=" O ASP g 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'g' and resid 148 through 152 removed outlier: 3.658A pdb=" N SER g 208 " --> pdb=" O CYS g 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR g 204 " --> pdb=" O ASP g 172 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER g 205 " --> pdb=" O VAL g 197 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'g' and resid 179 through 182 removed outlier: 3.781A pdb=" N CYS g 224 " --> pdb=" O LYS g 237 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS g 237 " --> pdb=" O CYS g 224 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.835A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.835A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.169A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.518A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.098A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.883A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 323 through 328 removed outlier: 7.008A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.784A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.613A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.534A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 713 through 723 removed outlier: 6.915A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 713 through 723 removed outlier: 6.915A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.411A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AG1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG2, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.759A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AG4, first strand: chain 'C' and resid 101 through 106 removed outlier: 3.806A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 117 through 121 removed outlier: 7.167A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 188 through 193 Processing sheet with id=AG7, first strand: chain 'C' and resid 188 through 193 removed outlier: 3.548A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.432A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 323 through 327 removed outlier: 4.251A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.615A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.531A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'C' and resid 551 through 552 removed outlier: 3.776A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.534A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.092A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.092A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.519A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 1120 through 1122 1306 hydrogen bonds defined for protein. 3456 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: 16.69 Time building geometry restraints manager: 14.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 10277 1.34 - 1.48: 8573 1.48 - 1.63: 15005 1.63 - 1.78: 24 1.78 - 1.92: 168 Bond restraints: 34047 Sorted by residual: bond pdb=" CA PRO B 384 " pdb=" C PRO B 384 " ideal model delta sigma weight residual 1.520 1.616 -0.096 1.42e-02 4.96e+03 4.60e+01 bond pdb=" CB THR d 219 " pdb=" CG2 THR d 219 " ideal model delta sigma weight residual 1.521 1.699 -0.178 3.30e-02 9.18e+02 2.91e+01 bond pdb=" CB THR H 219 " pdb=" CG2 THR H 219 " ideal model delta sigma weight residual 1.521 1.699 -0.178 3.30e-02 9.18e+02 2.90e+01 bond pdb=" CB THR g 219 " pdb=" CG2 THR g 219 " ideal model delta sigma weight residual 1.521 1.698 -0.177 3.30e-02 9.18e+02 2.88e+01 bond pdb=" CG ARG B 357 " pdb=" CD ARG B 357 " ideal model delta sigma weight residual 1.520 1.362 0.158 3.00e-02 1.11e+03 2.77e+01 ... (remaining 34042 not shown) Histogram of bond angle deviations from ideal: 71.84 - 88.79: 9 88.79 - 105.74: 997 105.74 - 122.69: 40431 122.69 - 139.64: 4879 139.64 - 156.58: 7 Bond angle restraints: 46323 Sorted by residual: angle pdb=" C LEU A 533 " pdb=" N VAL A 534 " pdb=" CA VAL A 534 " ideal model delta sigma weight residual 122.95 100.24 22.71 1.24e+00 6.50e-01 3.35e+02 angle pdb=" CB LYS L 188 " pdb=" CG LYS L 188 " pdb=" CD LYS L 188 " ideal model delta sigma weight residual 111.30 71.84 39.46 2.30e+00 1.89e-01 2.94e+02 angle pdb=" CB LYS c 188 " pdb=" CG LYS c 188 " pdb=" CD LYS c 188 " ideal model delta sigma weight residual 111.30 71.85 39.45 2.30e+00 1.89e-01 2.94e+02 angle pdb=" CB LYS f 188 " pdb=" CG LYS f 188 " pdb=" CD LYS f 188 " ideal model delta sigma weight residual 111.30 71.86 39.44 2.30e+00 1.89e-01 2.94e+02 angle pdb=" CB LEU g 102 " pdb=" CG LEU g 102 " pdb=" CD1 LEU g 102 " ideal model delta sigma weight residual 110.70 156.58 -45.88 3.00e+00 1.11e-01 2.34e+02 ... (remaining 46318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17582 17.95 - 35.91: 1687 35.91 - 53.86: 788 53.86 - 71.82: 214 71.82 - 89.77: 60 Dihedral angle restraints: 20331 sinusoidal: 7863 harmonic: 12468 Sorted by residual: dihedral pdb=" CA VAL B 382 " pdb=" C VAL B 382 " pdb=" N SER B 383 " pdb=" CA SER B 383 " ideal model delta harmonic sigma weight residual -180.00 -102.72 -77.28 0 5.00e+00 4.00e-02 2.39e+02 dihedral pdb=" CA TYR f 113 " pdb=" C TYR f 113 " pdb=" N PRO f 114 " pdb=" CA PRO f 114 " ideal model delta harmonic sigma weight residual -180.00 -117.26 -62.74 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA TYR c 113 " pdb=" C TYR c 113 " pdb=" N PRO c 114 " pdb=" CA PRO c 114 " ideal model delta harmonic sigma weight residual -180.00 -117.33 -62.67 0 5.00e+00 4.00e-02 1.57e+02 ... (remaining 20328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.269: 5173 0.269 - 0.537: 50 0.537 - 0.806: 15 0.806 - 1.075: 3 1.075 - 1.344: 3 Chirality restraints: 5244 Sorted by residual: chirality pdb=" CG LEU g 102 " pdb=" CB LEU g 102 " pdb=" CD1 LEU g 102 " pdb=" CD2 LEU g 102 " both_signs ideal model delta sigma weight residual False -2.59 -1.25 -1.34 2.00e-01 2.50e+01 4.51e+01 chirality pdb=" CG LEU d 102 " pdb=" CB LEU d 102 " pdb=" CD1 LEU d 102 " pdb=" CD2 LEU d 102 " both_signs ideal model delta sigma weight residual False -2.59 -1.25 -1.34 2.00e-01 2.50e+01 4.50e+01 chirality pdb=" CG LEU H 102 " pdb=" CB LEU H 102 " pdb=" CD1 LEU H 102 " pdb=" CD2 LEU H 102 " both_signs ideal model delta sigma weight residual False -2.59 -1.25 -1.34 2.00e-01 2.50e+01 4.50e+01 ... (remaining 5241 not shown) Planarity restraints: 5989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP f 51 " -0.056 2.00e-02 2.50e+03 4.58e-02 5.25e+01 pdb=" CG TRP f 51 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP f 51 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP f 51 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP f 51 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP f 51 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP f 51 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 51 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 51 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP f 51 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP c 51 " -0.056 2.00e-02 2.50e+03 4.57e-02 5.21e+01 pdb=" CG TRP c 51 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP c 51 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP c 51 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP c 51 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP c 51 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP c 51 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 51 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 51 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP c 51 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 51 " 0.056 2.00e-02 2.50e+03 4.55e-02 5.18e+01 pdb=" CG TRP L 51 " -0.122 2.00e-02 2.50e+03 pdb=" CD1 TRP L 51 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP L 51 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP L 51 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 51 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 51 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP L 51 " 0.007 2.00e-02 2.50e+03 ... (remaining 5986 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 8 2.03 - 2.75: 3992 2.75 - 3.47: 47324 3.47 - 4.18: 83418 4.18 - 4.90: 138421 Nonbonded interactions: 273163 Sorted by model distance: nonbonded pdb=" CA PRO A 230 " pdb=" NH2 ARG B 357 " model vdw 1.315 3.550 nonbonded pdb=" CE1 PHE C 133 " pdb=" CB ALA C 163 " model vdw 1.684 3.760 nonbonded pdb=" OH TYR A 200 " pdb=" ND2 ASN B 394 " model vdw 1.933 2.520 nonbonded pdb=" NE2 GLN f 166 " pdb=" OE1 GLU f 214 " model vdw 1.970 2.520 nonbonded pdb=" NE2 GLN L 166 " pdb=" OE1 GLU L 214 " model vdw 1.970 2.520 ... (remaining 273158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 228 or (resid 229 \ and (name N or name CA or name C or name O or name CB )) or resid 230 through 23 \ 2 or (resid 233 and (name N or name CA or name C or name O or name CB )) or resi \ d 234 through 274 or (resid 275 and (name N or name CA or name C or name O or na \ me CB )) or resid 276 through 327 or (resid 328 and (name N or name CA or name C \ or name O or name CB )) or resid 329 through 514 or resid 524 through 528 or (r \ esid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 t \ hrough 543 or resid 549 through 1146)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 54 or (resid 55 and (name N or nam \ e CA or name C or name O or name CB )) or resid 56 through 199 or (resid 200 and \ (name N or name CA or name C or name O or name CB )) or resid 201 through 228 o \ r (resid 229 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 30 through 232 or (resid 233 and (name N or name CA or name C or name O or name \ CB )) or resid 234 through 274 or (resid 275 and (name N or name CA or name C or \ name O or name CB )) or resid 276 through 327 or (resid 328 and (name N or name \ CA or name C or name O or name CB )) or resid 329 through 514 or resid 524 thro \ ugh 527 or (resid 528 through 529 and (name N or name CA or name C or name O or \ name CB )) or resid 530 through 543 or resid 549 through 564 or (resid 565 and ( \ name N or name CA or name C or name O or name CB )) or resid 566 or (resid 567 a \ nd (name N or name CA or name C or name O or name CB )) or resid 568 through 940 \ or resid 946 through 1146)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 514 or resid 524 through 564 or (r \ esid 565 and (name N or name CA or name C or name O or name CB )) or resid 566 o \ r (resid 567 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 68 through 940 or resid 946 through 1146)) } ncs_group { reference = chain 'H' selection = chain 'd' selection = chain 'g' } ncs_group { reference = chain 'L' selection = chain 'c' selection = chain 'f' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.510 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 91.060 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 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 : 0.011 0.178 34047 Z= 0.703 Angle : 1.808 45.884 46323 Z= 1.062 Chirality : 0.101 1.344 5244 Planarity : 0.009 0.139 5989 Dihedral : 18.609 89.772 12166 Min Nonbonded Distance : 1.315 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.32 % Favored : 88.76 % Rotamer: Outliers : 13.67 % Allowed : 6.38 % Favored : 79.96 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 4.93 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.27 % 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: -3.17 (0.12), residues: 4226 helix: -1.54 (0.17), residues: 702 sheet: -1.61 (0.15), residues: 1110 loop : -2.60 (0.11), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.006 TRP f 51 HIS 0.011 0.002 HIS B 519 PHE 0.101 0.004 PHE g 128 TYR 0.083 0.004 TYR f 113 ARG 0.071 0.003 ARG f 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 510 poor density : 822 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6599 (p0) REVERT: A 368 LEU cc_start: 0.7094 (mp) cc_final: 0.6707 (tp) REVERT: A 529 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5614 (mmmt) REVERT: A 564 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7137 (mt0) REVERT: A 752 LEU cc_start: 0.8591 (mt) cc_final: 0.7561 (mm) REVERT: A 816 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.9091 (t) REVERT: A 1104 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8610 (t) REVERT: A 1133 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7592 (t) REVERT: H 76 ASN cc_start: 0.7762 (m-40) cc_final: 0.7364 (t0) REVERT: H 99 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.5364 (m-10) REVERT: H 133 GLN cc_start: 0.4554 (OUTLIER) cc_final: 0.3502 (tp40) REVERT: L 106 TYR cc_start: 0.2600 (m-80) cc_final: 0.2324 (m-10) REVERT: L 206 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.5158 (mp0) REVERT: c 23 MET cc_start: 0.2410 (mtp) cc_final: 0.2076 (mmm) REVERT: c 66 LEU cc_start: 0.2507 (OUTLIER) cc_final: 0.1819 (mp) REVERT: c 202 LYS cc_start: 0.1974 (mmtm) cc_final: 0.0227 (tptt) REVERT: c 206 GLU cc_start: 0.3322 (OUTLIER) cc_final: 0.2984 (mp0) REVERT: c 230 ARG cc_start: 0.4314 (OUTLIER) cc_final: 0.2756 (mmp80) REVERT: d 22 GLN cc_start: 0.4304 (OUTLIER) cc_final: 0.3981 (tp-100) REVERT: d 79 TYR cc_start: 0.1186 (m-80) cc_final: 0.0923 (m-80) REVERT: d 216 SER cc_start: 0.4112 (OUTLIER) cc_final: 0.3796 (t) REVERT: f 73 LEU cc_start: 0.6964 (tp) cc_final: 0.6726 (tt) REVERT: f 141 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6613 (p0) REVERT: f 205 TYR cc_start: -0.0958 (t80) cc_final: -0.1234 (t80) REVERT: g 108 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5252 (pm20) REVERT: g 109 ASP cc_start: 0.6951 (m-30) cc_final: 0.5657 (t70) REVERT: g 113 TYR cc_start: 0.5697 (m-80) cc_final: 0.5184 (m-10) REVERT: B 101 ILE cc_start: 0.5733 (OUTLIER) cc_final: 0.5051 (pt) REVERT: B 540 ASN cc_start: 0.3015 (OUTLIER) cc_final: 0.1837 (t0) REVERT: B 816 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8499 (t) REVERT: B 823 PHE cc_start: 0.6281 (m-80) cc_final: 0.5846 (m-10) REVERT: C 36 VAL cc_start: 0.7220 (t) cc_final: 0.7002 (t) REVERT: C 141 LEU cc_start: 0.2740 (OUTLIER) cc_final: 0.2487 (pp) REVERT: C 215 ASP cc_start: 0.4124 (OUTLIER) cc_final: 0.3282 (t0) REVERT: C 238 PHE cc_start: 0.4958 (OUTLIER) cc_final: 0.4500 (p90) REVERT: C 341 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8511 (p) REVERT: C 377 PHE cc_start: 0.3858 (OUTLIER) cc_final: 0.3069 (m-80) REVERT: C 394 ASN cc_start: 0.7373 (p0) cc_final: 0.6997 (p0) REVERT: C 396 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: C 461 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.5617 (tp) REVERT: C 481 ASN cc_start: 0.4051 (OUTLIER) cc_final: 0.2981 (p0) REVERT: C 492 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7384 (mt) REVERT: C 524 VAL cc_start: 0.5270 (OUTLIER) cc_final: 0.5003 (t) REVERT: C 537 LYS cc_start: 0.3266 (OUTLIER) cc_final: 0.2736 (tmtt) outliers start: 510 outliers final: 71 residues processed: 1196 average time/residue: 0.4932 time to fit residues: 919.1170 Evaluate side-chains 470 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 369 time to evaluate : 4.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 206 GLU Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain c residue 61 LYS Chi-restraints excluded: chain c residue 66 LEU Chi-restraints excluded: chain c residue 86 SER Chi-restraints excluded: chain c residue 122 LYS Chi-restraints excluded: chain c residue 133 SER Chi-restraints excluded: chain c residue 206 GLU Chi-restraints excluded: chain c residue 209 LYS Chi-restraints excluded: chain c residue 230 ARG Chi-restraints excluded: chain d residue 22 GLN Chi-restraints excluded: chain d residue 36 SER Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain d residue 121 ARG Chi-restraints excluded: chain d residue 122 ARG Chi-restraints excluded: chain d residue 216 SER Chi-restraints excluded: chain f residue 61 LYS Chi-restraints excluded: chain f residue 66 LEU Chi-restraints excluded: chain f residue 141 ASP Chi-restraints excluded: chain g residue 22 GLN Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 96 SER Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain g residue 148 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 0.8980 chunk 323 optimal weight: 0.0050 chunk 179 optimal weight: 40.0000 chunk 110 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 334 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 387 optimal weight: 0.8980 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 370 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN A 762 GLN A 801 ASN ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 928 ASN A 954 GLN A 965 GLN A1005 GLN A1036 GLN A1135 ASN H 76 ASN H 227 ASN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 ASN c 46 GLN c 56 GLN ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 157 ASN ** c 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 ASN d 84 GLN d 192 HIS ** f 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN ** g 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 GLN B 165 ASN B 188 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 657 ASN B 709 ASN B 710 ASN B 751 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 965 GLN B1134 ASN C 115 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 613 GLN C 657 ASN C 762 GLN C 926 GLN C 928 ASN C 955 ASN C 965 GLN C1054 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 34047 Z= 0.322 Angle : 0.805 13.367 46323 Z= 0.422 Chirality : 0.049 0.314 5244 Planarity : 0.007 0.116 5989 Dihedral : 8.762 67.886 4796 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.69 % Favored : 92.10 % Rotamer: Outliers : 5.06 % Allowed : 15.43 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.12), residues: 4226 helix: 0.25 (0.19), residues: 680 sheet: -1.03 (0.15), residues: 1195 loop : -2.23 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 51 HIS 0.010 0.001 HIS C1083 PHE 0.025 0.002 PHE C 823 TYR 0.041 0.002 TYR L 110 ARG 0.013 0.001 ARG g 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 389 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6473 (ptmm) REVERT: A 1104 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8919 (t) REVERT: H 51 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.3587 (m-80) REVERT: H 100 MET cc_start: 0.4343 (ptm) cc_final: 0.3816 (ptp) REVERT: L 23 MET cc_start: 0.1204 (mmm) cc_final: 0.0658 (tpp) REVERT: L 106 TYR cc_start: 0.2461 (m-80) cc_final: 0.2248 (m-10) REVERT: L 113 TYR cc_start: 0.3679 (OUTLIER) cc_final: 0.3124 (m-80) REVERT: L 205 TYR cc_start: -0.1510 (OUTLIER) cc_final: -0.3005 (m-80) REVERT: c 51 TRP cc_start: 0.5598 (OUTLIER) cc_final: 0.5395 (m100) REVERT: c 209 LYS cc_start: 0.6288 (tptp) cc_final: 0.5216 (tmmt) REVERT: f 68 TYR cc_start: 0.7976 (p90) cc_final: 0.7500 (p90) REVERT: g 51 TYR cc_start: 0.4910 (OUTLIER) cc_final: 0.3569 (m-80) REVERT: g 54 HIS cc_start: 0.5532 (t-170) cc_final: 0.5177 (t70) REVERT: g 102 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6477 (tp) REVERT: B 133 PHE cc_start: 0.6369 (m-10) cc_final: 0.5984 (m-10) REVERT: B 215 ASP cc_start: -0.0648 (OUTLIER) cc_final: -0.1085 (t70) REVERT: B 296 LEU cc_start: 0.8424 (tt) cc_final: 0.7906 (tt) REVERT: B 497 PHE cc_start: 0.4702 (m-80) cc_final: 0.3995 (m-80) REVERT: B 508 TYR cc_start: 0.7179 (m-80) cc_final: 0.6782 (m-10) REVERT: B 514 SER cc_start: 0.8633 (t) cc_final: 0.8262 (p) REVERT: B 540 ASN cc_start: 0.3387 (OUTLIER) cc_final: 0.1874 (t0) REVERT: B 707 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7956 (p90) REVERT: C 91 TYR cc_start: 0.5397 (t80) cc_final: 0.4996 (t80) REVERT: C 238 PHE cc_start: 0.4925 (OUTLIER) cc_final: 0.4693 (p90) REVERT: C 341 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8514 (p) REVERT: C 377 PHE cc_start: 0.5373 (OUTLIER) cc_final: 0.4670 (m-80) REVERT: C 396 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6811 (m-80) REVERT: C 452 LEU cc_start: 0.8386 (mp) cc_final: 0.8107 (mp) REVERT: C 481 ASN cc_start: 0.4381 (OUTLIER) cc_final: 0.3069 (p0) REVERT: C 492 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7455 (mt) REVERT: C 613 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7481 (mm-40) REVERT: C 692 ILE cc_start: 0.7554 (mt) cc_final: 0.7019 (mm) REVERT: C 1005 GLN cc_start: 0.8134 (tp40) cc_final: 0.7710 (tp-100) outliers start: 189 outliers final: 97 residues processed: 544 average time/residue: 0.4395 time to fit residues: 388.5535 Evaluate side-chains 404 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 289 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 205 TYR Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 51 TRP Chi-restraints excluded: chain c residue 133 SER Chi-restraints excluded: chain c residue 141 ASP Chi-restraints excluded: chain c residue 186 ASP Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 86 SER Chi-restraints excluded: chain g residue 29 GLU Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 32 LYS Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 96 SER Chi-restraints excluded: chain g residue 102 LEU Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 215 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 322 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 388 optimal weight: 1.9990 chunk 419 optimal weight: 0.8980 chunk 345 optimal weight: 0.8980 chunk 385 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN A 762 GLN A 824 ASN A 955 ASN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 GLN L 208 HIS ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 143 GLN ** c 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 119 GLN ** f 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 208 HIS g 22 GLN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B1074 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34047 Z= 0.237 Angle : 0.689 11.334 46323 Z= 0.359 Chirality : 0.047 0.252 5244 Planarity : 0.006 0.075 5989 Dihedral : 6.789 60.056 4668 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.46 % Favored : 93.35 % Rotamer: Outliers : 4.42 % Allowed : 17.68 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.65 (0.13), residues: 4226 helix: 0.98 (0.20), residues: 675 sheet: -0.56 (0.15), residues: 1192 loop : -2.10 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP H 69 HIS 0.007 0.001 HIS L 208 PHE 0.040 0.002 PHE A 157 TYR 0.027 0.002 TYR c 159 ARG 0.011 0.001 ARG L 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 336 time to evaluate : 3.841 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: A 113 LYS cc_start: 0.5309 (OUTLIER) cc_final: 0.4733 (mtmm) REVERT: A 153 MET cc_start: 0.4771 (ptt) cc_final: 0.4187 (ptt) REVERT: A 408 ARG cc_start: 0.7043 (mpt180) cc_final: 0.6289 (tmm160) REVERT: A 529 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.6838 (ptmm) REVERT: A 1104 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8855 (t) REVERT: H 51 TYR cc_start: 0.3488 (OUTLIER) cc_final: 0.2511 (m-80) REVERT: H 100 MET cc_start: 0.4078 (ptm) cc_final: 0.3818 (ptm) REVERT: L 113 TYR cc_start: 0.4075 (OUTLIER) cc_final: 0.3028 (m-80) REVERT: L 166 GLN cc_start: 0.4884 (OUTLIER) cc_final: 0.4208 (mm-40) REVERT: c 209 LYS cc_start: 0.6020 (tptp) cc_final: 0.5071 (tmmt) REVERT: d 102 LEU cc_start: -0.1317 (OUTLIER) cc_final: -0.2563 (tp) REVERT: d 103 SER cc_start: 0.4688 (m) cc_final: 0.4407 (t) REVERT: f 68 TYR cc_start: 0.7960 (p90) cc_final: 0.7596 (p90) REVERT: g 29 GLU cc_start: 0.5078 (OUTLIER) cc_final: 0.4766 (tt0) REVERT: g 51 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.3336 (m-80) REVERT: g 122 ARG cc_start: 0.7642 (ttp-110) cc_final: 0.7142 (mtp180) REVERT: B 92 PHE cc_start: 0.6752 (t80) cc_final: 0.6483 (t80) REVERT: B 133 PHE cc_start: 0.6423 (m-10) cc_final: 0.6025 (m-10) REVERT: B 153 MET cc_start: 0.0960 (ttp) cc_final: 0.0745 (ttp) REVERT: B 215 ASP cc_start: -0.0428 (OUTLIER) cc_final: -0.1085 (t70) REVERT: B 274 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7733 (p) REVERT: B 508 TYR cc_start: 0.7292 (m-80) cc_final: 0.6924 (m-80) REVERT: B 514 SER cc_start: 0.8546 (t) cc_final: 0.8258 (p) REVERT: B 540 ASN cc_start: 0.3457 (OUTLIER) cc_final: 0.1819 (t0) REVERT: B 707 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.8074 (p90) REVERT: B 823 PHE cc_start: 0.6193 (m-80) cc_final: 0.5923 (m-80) REVERT: C 141 LEU cc_start: 0.3416 (OUTLIER) cc_final: 0.3164 (pp) REVERT: C 347 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.7095 (m-10) REVERT: C 377 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.5053 (m-80) REVERT: C 396 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: C 452 LEU cc_start: 0.8468 (mp) cc_final: 0.8121 (mp) REVERT: C 481 ASN cc_start: 0.4437 (OUTLIER) cc_final: 0.3301 (p0) REVERT: C 492 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7402 (mt) REVERT: C 606 ASN cc_start: 0.8477 (p0) cc_final: 0.8234 (p0) outliers start: 165 outliers final: 82 residues processed: 468 average time/residue: 0.4735 time to fit residues: 366.4794 Evaluate side-chains 383 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 282 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain c residue 141 ASP Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain g residue 29 GLU Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 383 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 chunk 201 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 389 optimal weight: 0.6980 chunk 412 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 369 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A 992 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 71 ASN d 192 HIS ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 208 HIS B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 764 ASN B 787 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN C 710 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 34047 Z= 0.299 Angle : 0.680 12.819 46323 Z= 0.351 Chirality : 0.046 0.239 5244 Planarity : 0.006 0.073 5989 Dihedral : 6.340 59.725 4645 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.44 % Favored : 93.42 % Rotamer: Outliers : 5.23 % Allowed : 18.14 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.56 (0.13), residues: 4226 helix: 1.07 (0.20), residues: 671 sheet: -0.56 (0.15), residues: 1246 loop : -2.03 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 69 HIS 0.006 0.001 HIS H 54 PHE 0.029 0.002 PHE C 559 TYR 0.027 0.002 TYR c 192 ARG 0.007 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 308 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.5317 (OUTLIER) cc_final: 0.4647 (mtmm) REVERT: A 408 ARG cc_start: 0.6973 (mpt180) cc_final: 0.6252 (tmm160) REVERT: A 546 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7441 (tt) REVERT: A 1104 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.8998 (t) REVERT: H 51 TYR cc_start: 0.3403 (OUTLIER) cc_final: 0.1682 (m-80) REVERT: L 113 TYR cc_start: 0.4523 (OUTLIER) cc_final: 0.3379 (m-80) REVERT: L 166 GLN cc_start: 0.4889 (OUTLIER) cc_final: 0.4247 (mm-40) REVERT: c 209 LYS cc_start: 0.5959 (tptp) cc_final: 0.5115 (tmmt) REVERT: d 53 MET cc_start: 0.0438 (tpp) cc_final: -0.0390 (tpt) REVERT: f 68 TYR cc_start: 0.7784 (p90) cc_final: 0.7435 (p90) REVERT: f 206 GLU cc_start: 0.3017 (OUTLIER) cc_final: 0.1377 (tp30) REVERT: g 51 TYR cc_start: 0.4995 (OUTLIER) cc_final: 0.3292 (m-80) REVERT: g 122 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7346 (mtp180) REVERT: B 133 PHE cc_start: 0.6229 (m-10) cc_final: 0.5561 (m-10) REVERT: B 215 ASP cc_start: -0.0174 (OUTLIER) cc_final: -0.1041 (t70) REVERT: B 514 SER cc_start: 0.8624 (t) cc_final: 0.8331 (p) REVERT: B 540 ASN cc_start: 0.4058 (OUTLIER) cc_final: 0.2400 (t0) REVERT: B 707 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8136 (p90) REVERT: C 141 LEU cc_start: 0.3779 (OUTLIER) cc_final: 0.3575 (pp) REVERT: C 234 ASN cc_start: 0.5173 (OUTLIER) cc_final: 0.4725 (m110) REVERT: C 377 PHE cc_start: 0.6131 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: C 429 PHE cc_start: 0.7756 (t80) cc_final: 0.7550 (t80) REVERT: C 452 LEU cc_start: 0.8560 (mp) cc_final: 0.8342 (mp) REVERT: C 481 ASN cc_start: 0.4677 (OUTLIER) cc_final: 0.3648 (p0) REVERT: C 492 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7347 (mt) outliers start: 195 outliers final: 122 residues processed: 477 average time/residue: 0.4805 time to fit residues: 378.2411 Evaluate side-chains 402 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 264 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain c residue 141 ASP Chi-restraints excluded: chain c residue 210 VAL Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 206 GLU Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 121 ARG Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 343 optimal weight: 0.2980 chunk 234 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 307 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 352 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 926 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 HIS ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 GLN ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS f 25 GLN ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 208 HIS B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34047 Z= 0.301 Angle : 0.669 13.038 46323 Z= 0.344 Chirality : 0.046 0.229 5244 Planarity : 0.005 0.074 5989 Dihedral : 6.145 58.858 4638 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.46 % Favored : 93.40 % Rotamer: Outliers : 5.01 % Allowed : 19.48 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.45 (0.13), residues: 4226 helix: 1.16 (0.20), residues: 677 sheet: -0.41 (0.15), residues: 1208 loop : -2.00 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 353 HIS 0.007 0.001 HIS H 54 PHE 0.039 0.002 PHE C 456 TYR 0.027 0.002 TYR c 159 ARG 0.008 0.001 ARG L 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 288 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 THR cc_start: -0.2318 (OUTLIER) cc_final: -0.2698 (p) REVERT: A 529 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7428 (mmtp) REVERT: A 546 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7449 (tt) REVERT: A 1104 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8947 (t) REVERT: H 51 TYR cc_start: 0.3818 (OUTLIER) cc_final: 0.1963 (m-80) REVERT: L 113 TYR cc_start: 0.4408 (OUTLIER) cc_final: 0.2920 (m-80) REVERT: c 209 LYS cc_start: 0.5750 (tptp) cc_final: 0.5195 (tmmt) REVERT: d 53 MET cc_start: 0.0585 (tpp) cc_final: -0.0214 (tpt) REVERT: d 103 SER cc_start: 0.4766 (m) cc_final: 0.4467 (t) REVERT: f 68 TYR cc_start: 0.7843 (p90) cc_final: 0.7505 (p90) REVERT: f 113 TYR cc_start: 0.3511 (OUTLIER) cc_final: 0.2901 (m-80) REVERT: f 206 GLU cc_start: 0.3080 (OUTLIER) cc_final: 0.1829 (tp30) REVERT: g 51 TYR cc_start: 0.5172 (OUTLIER) cc_final: 0.3306 (m-80) REVERT: g 67 MET cc_start: 0.5538 (mmm) cc_final: 0.5321 (mmm) REVERT: g 122 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7296 (mtt-85) REVERT: B 133 PHE cc_start: 0.6397 (m-10) cc_final: 0.5595 (m-10) REVERT: B 215 ASP cc_start: -0.0098 (OUTLIER) cc_final: -0.1125 (t70) REVERT: B 514 SER cc_start: 0.8639 (t) cc_final: 0.8315 (p) REVERT: B 540 ASN cc_start: 0.4892 (OUTLIER) cc_final: 0.2837 (t0) REVERT: B 707 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.8183 (p90) REVERT: C 104 TRP cc_start: 0.5264 (p90) cc_final: 0.4868 (p90) REVERT: C 234 ASN cc_start: 0.5274 (OUTLIER) cc_final: 0.4926 (m110) REVERT: C 377 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5377 (m-80) REVERT: C 481 ASN cc_start: 0.4852 (OUTLIER) cc_final: 0.3793 (p0) REVERT: C 492 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7472 (mt) outliers start: 187 outliers final: 123 residues processed: 449 average time/residue: 0.4245 time to fit residues: 315.3873 Evaluate side-chains 398 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 259 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain c residue 159 TYR Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 206 GLU Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 91 ARG Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 138 optimal weight: 30.0000 chunk 371 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 413 optimal weight: 0.9980 chunk 342 optimal weight: 9.9990 chunk 191 optimal weight: 40.0000 chunk 34 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 115 GLN A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 926 GLN A 992 GLN A1011 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 HIS ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS f 22 GLN f 56 GLN ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 143 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34047 Z= 0.273 Angle : 0.651 12.812 46323 Z= 0.335 Chirality : 0.046 0.235 5244 Planarity : 0.005 0.072 5989 Dihedral : 5.997 57.769 4638 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.53 % Favored : 93.33 % Rotamer: Outliers : 5.06 % Allowed : 19.77 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.38 (0.13), residues: 4226 helix: 1.22 (0.20), residues: 678 sheet: -0.46 (0.15), residues: 1230 loop : -1.90 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 69 HIS 0.005 0.001 HIS H 54 PHE 0.038 0.002 PHE C 456 TYR 0.019 0.002 TYR B1067 ARG 0.007 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 274 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 THR cc_start: -0.2348 (OUTLIER) cc_final: -0.2730 (p) REVERT: A 529 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7653 (mmtm) REVERT: A 546 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7487 (tt) REVERT: A 1104 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8952 (t) REVERT: H 51 TYR cc_start: 0.3344 (OUTLIER) cc_final: 0.1231 (m-80) REVERT: L 113 TYR cc_start: 0.4330 (OUTLIER) cc_final: 0.2817 (m-80) REVERT: L 161 ARG cc_start: 0.7477 (mmt180) cc_final: 0.6816 (mmt180) REVERT: L 166 GLN cc_start: 0.5026 (OUTLIER) cc_final: 0.4389 (mm-40) REVERT: c 209 LYS cc_start: 0.5612 (tptp) cc_final: 0.5159 (tmmt) REVERT: d 53 MET cc_start: 0.0588 (tpp) cc_final: -0.0071 (tpt) REVERT: d 103 SER cc_start: 0.4456 (m) cc_final: 0.4116 (t) REVERT: f 68 TYR cc_start: 0.7775 (p90) cc_final: 0.7430 (p90) REVERT: f 113 TYR cc_start: 0.4193 (OUTLIER) cc_final: 0.3476 (m-80) REVERT: f 206 GLU cc_start: 0.3296 (OUTLIER) cc_final: 0.2122 (tp30) REVERT: g 51 TYR cc_start: 0.5332 (OUTLIER) cc_final: 0.3376 (m-80) REVERT: g 122 ARG cc_start: 0.7816 (ttp-110) cc_final: 0.7316 (mtt-85) REVERT: B 133 PHE cc_start: 0.6325 (m-10) cc_final: 0.5525 (m-10) REVERT: B 215 ASP cc_start: -0.0068 (OUTLIER) cc_final: -0.0820 (t70) REVERT: B 514 SER cc_start: 0.8637 (t) cc_final: 0.8313 (p) REVERT: B 984 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 104 TRP cc_start: 0.5123 (p90) cc_final: 0.4589 (p90) REVERT: C 377 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5344 (m-80) REVERT: C 481 ASN cc_start: 0.4416 (OUTLIER) cc_final: 0.3673 (p0) REVERT: C 492 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7467 (mt) outliers start: 189 outliers final: 129 residues processed: 439 average time/residue: 0.4412 time to fit residues: 320.4456 Evaluate side-chains 395 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 251 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 128 PHE Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain c residue 141 ASP Chi-restraints excluded: chain c residue 159 TYR Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 206 GLU Chi-restraints excluded: chain f residue 222 SER Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 71 ASN Chi-restraints excluded: chain g residue 91 ARG Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 398 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 301 optimal weight: 0.8980 chunk 233 optimal weight: 20.0000 chunk 347 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 411 optimal weight: 0.0570 chunk 257 optimal weight: 9.9990 chunk 250 optimal weight: 0.9980 chunk 190 optimal weight: 0.4980 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.6746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34047 Z= 0.180 Angle : 0.616 14.962 46323 Z= 0.315 Chirality : 0.045 0.229 5244 Planarity : 0.005 0.071 5989 Dihedral : 5.610 58.772 4635 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.87 % Favored : 93.99 % Rotamer: Outliers : 3.99 % Allowed : 21.28 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.16 (0.13), residues: 4226 helix: 1.62 (0.21), residues: 671 sheet: -0.39 (0.15), residues: 1222 loop : -1.76 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 115 HIS 0.011 0.001 HIS d 54 PHE 0.033 0.001 PHE C 456 TYR 0.024 0.001 TYR L 113 ARG 0.006 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 272 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 THR cc_start: -0.2379 (OUTLIER) cc_final: -0.2743 (p) REVERT: A 546 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7397 (tt) REVERT: A 1104 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8878 (t) REVERT: H 51 TYR cc_start: 0.3215 (OUTLIER) cc_final: 0.0900 (m-80) REVERT: L 113 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.3129 (m-80) REVERT: L 161 ARG cc_start: 0.7505 (mmt180) cc_final: 0.6851 (mmt180) REVERT: L 166 GLN cc_start: 0.4969 (OUTLIER) cc_final: 0.4279 (mm-40) REVERT: c 209 LYS cc_start: 0.5559 (tptp) cc_final: 0.5149 (tmmt) REVERT: d 103 SER cc_start: 0.4703 (m) cc_final: 0.4498 (t) REVERT: f 68 TYR cc_start: 0.7900 (p90) cc_final: 0.7573 (p90) REVERT: f 206 GLU cc_start: 0.3317 (OUTLIER) cc_final: 0.1746 (tp30) REVERT: g 51 TYR cc_start: 0.5389 (OUTLIER) cc_final: 0.3322 (m-80) REVERT: g 122 ARG cc_start: 0.7767 (ttp-110) cc_final: 0.7366 (mtt-85) REVERT: B 133 PHE cc_start: 0.6380 (m-10) cc_final: 0.5581 (m-10) REVERT: B 215 ASP cc_start: 0.0272 (OUTLIER) cc_final: -0.0618 (t0) REVERT: B 514 SER cc_start: 0.8631 (t) cc_final: 0.8281 (p) REVERT: B 770 ILE cc_start: 0.9116 (pt) cc_final: 0.8711 (mt) REVERT: B 984 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8023 (mp) REVERT: C 266 TYR cc_start: 0.4200 (m-80) cc_final: 0.3968 (m-80) REVERT: C 377 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: C 429 PHE cc_start: 0.7876 (t80) cc_final: 0.7675 (t80) REVERT: C 430 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8610 (t) REVERT: C 492 LEU cc_start: 0.7766 (tp) cc_final: 0.7535 (mt) outliers start: 149 outliers final: 98 residues processed: 403 average time/residue: 0.4351 time to fit residues: 289.9101 Evaluate side-chains 362 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 252 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain c residue 159 TYR Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 206 GLU Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 91 ARG Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 254 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 323 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 992 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS f 22 GLN ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.6945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34047 Z= 0.184 Angle : 0.620 14.061 46323 Z= 0.317 Chirality : 0.044 0.300 5244 Planarity : 0.005 0.071 5989 Dihedral : 5.332 59.020 4625 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.20 % Favored : 93.66 % Rotamer: Outliers : 3.70 % Allowed : 21.78 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.06 (0.13), residues: 4226 helix: 1.72 (0.21), residues: 670 sheet: -0.32 (0.15), residues: 1222 loop : -1.71 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP L 115 HIS 0.009 0.001 HIS A1064 PHE 0.038 0.001 PHE C 135 TYR 0.022 0.001 TYR C 612 ARG 0.006 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 271 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.8750 (mm) cc_final: 0.8535 (tp) REVERT: A 546 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7424 (tt) REVERT: A 1104 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8932 (p) REVERT: H 51 TYR cc_start: 0.3237 (OUTLIER) cc_final: 0.1270 (m-80) REVERT: L 113 TYR cc_start: 0.4258 (OUTLIER) cc_final: 0.3103 (m-80) REVERT: L 166 GLN cc_start: 0.4963 (OUTLIER) cc_final: 0.4260 (mm-40) REVERT: c 209 LYS cc_start: 0.5503 (tptp) cc_final: 0.5096 (pttm) REVERT: d 103 SER cc_start: 0.4687 (m) cc_final: 0.4480 (t) REVERT: f 68 TYR cc_start: 0.7849 (p90) cc_final: 0.7570 (p90) REVERT: f 113 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.3957 (m-80) REVERT: g 51 TYR cc_start: 0.5311 (OUTLIER) cc_final: 0.3259 (m-80) REVERT: g 100 MET cc_start: 0.7142 (ptm) cc_final: 0.6896 (ptm) REVERT: g 122 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7401 (mtt-85) REVERT: B 133 PHE cc_start: 0.6370 (m-10) cc_final: 0.5547 (m-10) REVERT: B 215 ASP cc_start: 0.0312 (OUTLIER) cc_final: -0.0605 (t0) REVERT: B 514 SER cc_start: 0.8620 (t) cc_final: 0.8264 (p) REVERT: B 712 ILE cc_start: 0.8800 (mt) cc_final: 0.8527 (mt) REVERT: B 770 ILE cc_start: 0.9139 (pt) cc_final: 0.8738 (mt) REVERT: B 984 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8035 (mp) REVERT: C 201 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6831 (t80) REVERT: C 377 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.5227 (m-80) REVERT: C 492 LEU cc_start: 0.7813 (tp) cc_final: 0.7350 (mt) outliers start: 138 outliers final: 101 residues processed: 393 average time/residue: 0.4320 time to fit residues: 281.1827 Evaluate side-chains 369 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 257 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain c residue 159 TYR Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 70 ILE Chi-restraints excluded: chain g residue 71 ASN Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 374 optimal weight: 6.9990 chunk 394 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 383 optimal weight: 0.1980 chunk 230 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 362 optimal weight: 10.0000 chunk 382 optimal weight: 9.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.7508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 34047 Z= 0.427 Angle : 0.748 13.888 46323 Z= 0.384 Chirality : 0.049 0.214 5244 Planarity : 0.006 0.106 5989 Dihedral : 5.882 54.113 4618 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.88 % Favored : 92.00 % Rotamer: Outliers : 4.45 % Allowed : 21.14 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.53 (0.13), residues: 4226 helix: 1.00 (0.20), residues: 672 sheet: -0.58 (0.15), residues: 1222 loop : -1.93 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP L 115 HIS 0.011 0.002 HIS H 54 PHE 0.038 0.002 PHE C 456 TYR 0.025 0.002 TYR B1067 ARG 0.005 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 248 time to evaluate : 3.615 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: A 546 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7642 (tt) REVERT: H 51 TYR cc_start: 0.2906 (OUTLIER) cc_final: 0.0812 (m-80) REVERT: L 113 TYR cc_start: 0.4270 (OUTLIER) cc_final: 0.3078 (m-80) REVERT: L 166 GLN cc_start: 0.5158 (OUTLIER) cc_final: 0.4508 (mm-40) REVERT: c 21 ILE cc_start: 0.3850 (mt) cc_final: 0.3430 (mt) REVERT: c 23 MET cc_start: 0.4202 (mmm) cc_final: 0.3577 (ptp) REVERT: c 209 LYS cc_start: 0.5548 (tptp) cc_final: 0.5101 (pttm) REVERT: d 103 SER cc_start: 0.4647 (m) cc_final: 0.4339 (t) REVERT: f 68 TYR cc_start: 0.7962 (p90) cc_final: 0.7720 (p90) REVERT: g 51 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.3247 (m-80) REVERT: g 77 THR cc_start: 0.5288 (p) cc_final: 0.5051 (t) REVERT: g 122 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7452 (mtt-85) REVERT: B 133 PHE cc_start: 0.6437 (m-10) cc_final: 0.5401 (m-10) REVERT: B 514 SER cc_start: 0.8649 (t) cc_final: 0.8292 (p) REVERT: B 534 VAL cc_start: 0.6783 (OUTLIER) cc_final: 0.6442 (m) REVERT: B 979 ASP cc_start: 0.7838 (m-30) cc_final: 0.7306 (t0) REVERT: B 984 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8200 (mp) REVERT: C 201 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7290 (t80) REVERT: C 377 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5386 (m-80) outliers start: 166 outliers final: 118 residues processed: 393 average time/residue: 0.3980 time to fit residues: 262.6153 Evaluate side-chains 363 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 236 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain c residue 210 VAL Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 70 ILE Chi-restraints excluded: chain g residue 71 ASN Chi-restraints excluded: chain g residue 91 ARG Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 2.9990 chunk 405 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 425 optimal weight: 6.9990 chunk 391 optimal weight: 0.9980 chunk 338 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 261 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 56 GLN ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 157 ASN ** f 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 613 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.7617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34047 Z= 0.225 Angle : 0.656 14.989 46323 Z= 0.335 Chirality : 0.045 0.197 5244 Planarity : 0.005 0.105 5989 Dihedral : 5.533 54.798 4617 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.08 % Favored : 93.80 % Rotamer: Outliers : 3.24 % Allowed : 22.11 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.34 (0.13), residues: 4226 helix: 1.12 (0.20), residues: 707 sheet: -0.46 (0.14), residues: 1277 loop : -1.86 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP L 115 HIS 0.007 0.001 HIS A1064 PHE 0.039 0.002 PHE C 135 TYR 0.024 0.002 TYR L 192 ARG 0.005 0.001 ARG L 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 259 time to evaluate : 3.940 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: A 546 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7527 (tt) REVERT: H 51 TYR cc_start: 0.2645 (OUTLIER) cc_final: 0.0509 (m-80) REVERT: H 55 TRP cc_start: 0.1366 (m100) cc_final: 0.1130 (m100) REVERT: H 58 GLN cc_start: 0.4727 (OUTLIER) cc_final: 0.4225 (tp40) REVERT: L 113 TYR cc_start: 0.4706 (OUTLIER) cc_final: 0.3629 (m-80) REVERT: L 166 GLN cc_start: 0.5108 (OUTLIER) cc_final: 0.4422 (mm-40) REVERT: c 23 MET cc_start: 0.4261 (mmm) cc_final: 0.3542 (ptp) REVERT: c 209 LYS cc_start: 0.5551 (tptp) cc_final: 0.5120 (pttm) REVERT: d 103 SER cc_start: 0.4397 (m) cc_final: 0.4112 (t) REVERT: f 68 TYR cc_start: 0.7950 (p90) cc_final: 0.7654 (p90) REVERT: g 51 TYR cc_start: 0.5349 (OUTLIER) cc_final: 0.3536 (m-80) REVERT: g 100 MET cc_start: 0.7228 (ptm) cc_final: 0.6835 (ptm) REVERT: g 122 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7380 (mtt-85) REVERT: B 133 PHE cc_start: 0.6355 (m-10) cc_final: 0.5512 (m-10) REVERT: B 153 MET cc_start: 0.1695 (ttp) cc_final: 0.1188 (ttp) REVERT: B 514 SER cc_start: 0.8615 (t) cc_final: 0.8260 (p) REVERT: B 770 ILE cc_start: 0.9186 (pt) cc_final: 0.8712 (mt) REVERT: B 984 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 201 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.7185 (t80) REVERT: C 377 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.5262 (m-80) REVERT: C 395 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7818 (p) outliers start: 121 outliers final: 98 residues processed: 365 average time/residue: 0.4514 time to fit residues: 271.3591 Evaluate side-chains 351 residues out of total 3744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 243 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain c residue 159 TYR Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 208 HIS Chi-restraints excluded: chain f residue 211 TYR Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 70 ILE Chi-restraints excluded: chain g residue 71 ASN Chi-restraints excluded: chain g residue 91 ARG Chi-restraints excluded: chain g residue 101 GLU Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 269 optimal weight: 20.0000 chunk 360 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 312 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 339 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 348 optimal weight: 0.0970 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.127347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.087444 restraints weight = 108365.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085214 restraints weight = 69346.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.084949 restraints weight = 57196.813| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.458 34047 Z= 0.419 Angle : 0.816 59.170 46323 Z= 0.476 Chirality : 0.047 0.634 5244 Planarity : 0.006 0.183 5989 Dihedral : 5.502 54.770 4614 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 3.24 % Allowed : 22.32 % Favored : 74.44 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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: -1.33 (0.13), residues: 4226 helix: 1.11 (0.20), residues: 707 sheet: -0.44 (0.14), residues: 1265 loop : -1.86 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP B 436 HIS 0.033 0.002 HIS g 54 PHE 0.056 0.002 PHE C 106 TYR 0.074 0.002 TYR C 380 ARG 0.010 0.001 ARG g 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7884.29 seconds wall clock time: 143 minutes 43.22 seconds (8623.22 seconds total)