Starting phenix.real_space_refine on Tue Jul 23 17:33:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/07_2024/9bry_44845.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/07_2024/9bry_44845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/07_2024/9bry_44845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/07_2024/9bry_44845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/07_2024/9bry_44845.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/07_2024/9bry_44845.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.044 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 160 5.16 5 C 15403 2.51 5 N 3780 2.21 5 O 4187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 287": "OE1" <-> "OE2" Residue "c GLU 308": "OE1" <-> "OE2" Residue "b PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 44": "OE1" <-> "OE2" Residue "d PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 42": "OE1" <-> "OE2" Residue "d GLU 83": "OE1" <-> "OE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 126": "OE1" <-> "OE2" Residue "d ASP 174": "OD1" <-> "OD2" Residue "d ASP 176": "OD1" <-> "OD2" Residue "d GLU 215": "OE1" <-> "OE2" Residue "d GLU 252": "OE1" <-> "OE2" Residue "d GLU 275": "OE1" <-> "OE2" Residue "d GLU 300": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "g GLU 50": "OE1" <-> "OE2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "h GLU 139": "OE1" <-> "OE2" Residue "i GLU 9": "OE1" <-> "OE2" Residue "k GLU 9": "OE1" <-> "OE2" Residue "k GLU 50": "OE1" <-> "OE2" Residue "m GLU 50": "OE1" <-> "OE2" Residue "n GLU 50": "OE1" <-> "OE2" Residue "o GLU 139": "OE1" <-> "OE2" Residue "a GLU 20": "OE1" <-> "OE2" Residue "a GLU 54": "OE1" <-> "OE2" Residue "a GLU 69": "OE1" <-> "OE2" Residue "a GLU 102": "OE1" <-> "OE2" Residue "a GLU 201": "OE1" <-> "OE2" Residue "a GLU 207": "OE1" <-> "OE2" Residue "a GLU 322": "OE1" <-> "OE2" Residue "a GLU 436": "OE1" <-> "OE2" Residue "a GLU 438": "OE1" <-> "OE2" Residue "a GLU 576": "OE1" <-> "OE2" Residue "a GLU 623": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23530 Number of models: 1 Model: "" Number of chains: 20 Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "f" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 666 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "e" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "a" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6039 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 31, 'TRANS': 711} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.98, per 1000 atoms: 0.55 Number of scatterers: 23530 At special positions: 0 Unit cell: (159.322, 126.13, 136.087, 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 160 16.00 O 4187 8.00 N 3780 7.00 C 15403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " NAG A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN c 351 " " NAG B 1 " - " ASN c 344 " " NAG C 1 " - " ASN c 267 " " NAG c 501 " - " ASN c 290 " " NAG c 503 " - " ASN c 297 " " NAG c 504 " - " ASN c 255 " " NAG c 505 " - " ASN c 399 " Time building additional restraints: 9.85 Conformation dependent library (CDL) restraints added in 4.3 seconds 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 6 sheets defined 76.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'c' and resid 418 through 442 removed outlier: 3.616A pdb=" N ILE c 432 " --> pdb=" O PHE c 428 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 30 Processing helix chain 'b' and resid 37 through 45 removed outlier: 3.634A pdb=" N PHE b 41 " --> pdb=" O ASP b 37 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR b 45 " --> pdb=" O PHE b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 81 removed outlier: 3.740A pdb=" N TRP b 50 " --> pdb=" O SER b 46 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE b 59 " --> pdb=" O ILE b 55 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER b 62 " --> pdb=" O ALA b 58 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER b 76 " --> pdb=" O ILE b 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 91 removed outlier: 4.145A pdb=" N LYS b 90 " --> pdb=" O ARG b 86 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN b 91 " --> pdb=" O ILE b 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 86 through 91' Processing helix chain 'b' and resid 92 through 114 removed outlier: 4.115A pdb=" N ALA b 102 " --> pdb=" O CYS b 98 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN b 114 " --> pdb=" O ILE b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 128 removed outlier: 3.705A pdb=" N GLY b 128 " --> pdb=" O PRO b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 168 removed outlier: 4.041A pdb=" N TYR b 132 " --> pdb=" O GLY b 128 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA b 168 " --> pdb=" O ALA b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 185 removed outlier: 5.377A pdb=" N ILE b 179 " --> pdb=" O VAL b 175 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL b 180 " --> pdb=" O LYS b 176 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU b 181 " --> pdb=" O ILE b 177 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER b 185 " --> pdb=" O GLU b 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 185 through 199 removed outlier: 3.918A pdb=" N THR b 199 " --> pdb=" O ALA b 195 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 10 removed outlier: 3.835A pdb=" N LEU d 9 " --> pdb=" O PHE d 5 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR d 10 " --> pdb=" O PHE d 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 5 through 10' Processing helix chain 'd' and resid 11 through 27 removed outlier: 6.795A pdb=" N TYR d 17 " --> pdb=" O VAL d 13 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU d 18 " --> pdb=" O ASP d 14 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA d 27 " --> pdb=" O ARG d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 39 Processing helix chain 'd' and resid 43 through 53 Processing helix chain 'd' and resid 68 through 90 removed outlier: 3.606A pdb=" N ILE d 72 " --> pdb=" O THR d 68 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS d 90 " --> pdb=" O HIS d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 120 removed outlier: 4.270A pdb=" N SER d 105 " --> pdb=" O PHE d 101 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR d 106 " --> pdb=" O ILE d 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU d 119 " --> pdb=" O ILE d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 131 removed outlier: 3.793A pdb=" N LYS d 130 " --> pdb=" O GLU d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 136 Processing helix chain 'd' and resid 140 through 146 removed outlier: 3.618A pdb=" N VAL d 143 " --> pdb=" O MET d 140 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN d 144 " --> pdb=" O GLU d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 158 removed outlier: 3.996A pdb=" N VAL d 158 " --> pdb=" O ASN d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 166 Processing helix chain 'd' and resid 179 through 203 Processing helix chain 'd' and resid 204 through 229 Proline residue: d 212 - end of helix Processing helix chain 'd' and resid 235 through 242 Processing helix chain 'd' and resid 251 through 256 Processing helix chain 'd' and resid 257 through 260 Processing helix chain 'd' and resid 262 through 272 removed outlier: 3.639A pdb=" N VAL d 266 " --> pdb=" O ASP d 262 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR d 272 " --> pdb=" O ASN d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 273 through 283 removed outlier: 3.596A pdb=" N LEU d 279 " --> pdb=" O GLU d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 291 through 308 removed outlier: 3.601A pdb=" N ARG d 295 " --> pdb=" O THR d 291 " (cutoff:3.500A) Processing helix chain 'd' and resid 315 through 340 removed outlier: 4.379A pdb=" N ALA d 319 " --> pdb=" O GLY d 315 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 37 removed outlier: 4.754A pdb=" N CYS f 14 " --> pdb=" O LYS f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 89 removed outlier: 4.028A pdb=" N ASN f 68 " --> pdb=" O GLN f 64 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS f 69 " --> pdb=" O VAL f 65 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE f 70 " --> pdb=" O SER f 66 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE f 71 " --> pdb=" O TYR f 67 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU f 89 " --> pdb=" O CYS f 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 46 removed outlier: 4.358A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET g 23 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 50 No H-bonds generated for 'chain 'g' and resid 48 through 50' Processing helix chain 'g' and resid 51 through 56 Processing helix chain 'g' and resid 56 through 74 removed outlier: 3.997A pdb=" N ILE g 65 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE g 67 " --> pdb=" O GLY g 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL g 72 " --> pdb=" O TYR g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 79 Processing helix chain 'g' and resid 85 through 122 removed outlier: 3.765A pdb=" N ALA g 122 " --> pdb=" O VAL g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 126 through 152 removed outlier: 4.533A pdb=" N GLY g 130 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE g 137 " --> pdb=" O LEU g 133 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY g 142 " --> pdb=" O ALA g 138 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY g 145 " --> pdb=" O LEU g 141 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA g 149 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 10 No H-bonds generated for 'chain 'h' and resid 8 through 10' Processing helix chain 'h' and resid 11 through 44 removed outlier: 4.194A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N MET h 23 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET h 28 " --> pdb=" O VAL h 24 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR h 34 " --> pdb=" O ALA h 30 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS h 36 " --> pdb=" O TYR h 32 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY h 38 " --> pdb=" O THR h 34 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET h 44 " --> pdb=" O GLY h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 Processing helix chain 'h' and resid 56 through 79 removed outlier: 3.638A pdb=" N VAL h 60 " --> pdb=" O ILE h 56 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL h 72 " --> pdb=" O TYR h 68 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 121 removed outlier: 4.100A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 126 through 153 removed outlier: 4.008A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU h 133 " --> pdb=" O VAL h 129 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE h 136 " --> pdb=" O ILE h 132 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU h 141 " --> pdb=" O PHE h 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY h 142 " --> pdb=" O ALA h 138 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 10 No H-bonds generated for 'chain 'i' and resid 8 through 10' Processing helix chain 'i' and resid 11 through 45 removed outlier: 3.861A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA i 19 " --> pdb=" O GLY i 15 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR i 39 " --> pdb=" O ALA i 35 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY i 40 " --> pdb=" O LYS i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 55 removed outlier: 3.913A pdb=" N ILE i 52 " --> pdb=" O PRO i 49 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET i 53 " --> pdb=" O GLU i 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS i 54 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 56 through 78 removed outlier: 3.541A pdb=" N GLY i 69 " --> pdb=" O ILE i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 121 Processing helix chain 'i' and resid 122 through 123 No H-bonds generated for 'chain 'i' and resid 122 through 123' Processing helix chain 'i' and resid 124 through 126 No H-bonds generated for 'chain 'i' and resid 124 through 126' Processing helix chain 'i' and resid 127 through 153 removed outlier: 4.297A pdb=" N LEU i 141 " --> pdb=" O PHE i 137 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY i 142 " --> pdb=" O ALA i 138 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU i 143 " --> pdb=" O GLU i 139 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL i 148 " --> pdb=" O TYR i 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 45 removed outlier: 4.153A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA j 19 " --> pdb=" O GLY j 15 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 54 removed outlier: 4.301A pdb=" N MET j 53 " --> pdb=" O GLU j 50 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 61 Processing helix chain 'j' and resid 63 through 79 removed outlier: 3.644A pdb=" N ILE j 67 " --> pdb=" O GLY j 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU j 75 " --> pdb=" O VAL j 71 " (cutoff:3.500A) Processing helix chain 'j' and resid 85 through 121 Processing helix chain 'j' and resid 126 through 155 removed outlier: 4.453A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET j 131 " --> pdb=" O LEU j 127 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE j 132 " --> pdb=" O PHE j 128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE j 137 " --> pdb=" O LEU j 133 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY j 142 " --> pdb=" O ALA j 138 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL j 148 " --> pdb=" O TYR j 144 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS j 155 " --> pdb=" O ILE j 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 11 removed outlier: 3.595A pdb=" N SER k 11 " --> pdb=" O PRO k 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 8 through 11' Processing helix chain 'k' and resid 12 through 45 removed outlier: 3.565A pdb=" N VAL k 16 " --> pdb=" O SER k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 47 No H-bonds generated for 'chain 'k' and resid 46 through 47' Processing helix chain 'k' and resid 48 through 52 removed outlier: 3.592A pdb=" N LEU k 51 " --> pdb=" O ARG k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 79 removed outlier: 3.581A pdb=" N VAL k 60 " --> pdb=" O ILE k 56 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE k 65 " --> pdb=" O MET k 61 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) Processing helix chain 'k' and resid 85 through 122 removed outlier: 3.545A pdb=" N SER k 89 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA k 122 " --> pdb=" O VAL k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 123 through 125 No H-bonds generated for 'chain 'k' and resid 123 through 125' Processing helix chain 'k' and resid 126 through 150 removed outlier: 4.353A pdb=" N GLY k 130 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE k 132 " --> pdb=" O PHE k 128 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU k 141 " --> pdb=" O PHE k 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY k 142 " --> pdb=" O ALA k 138 " (cutoff:3.500A) Processing helix chain 'k' and resid 150 through 155 Processing helix chain 'l' and resid 8 through 10 No H-bonds generated for 'chain 'l' and resid 8 through 10' Processing helix chain 'l' and resid 11 through 45 removed outlier: 4.365A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER l 26 " --> pdb=" O ALA l 22 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR l 39 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 47 No H-bonds generated for 'chain 'l' and resid 46 through 47' Processing helix chain 'l' and resid 48 through 50 No H-bonds generated for 'chain 'l' and resid 48 through 50' Processing helix chain 'l' and resid 51 through 56 Processing helix chain 'l' and resid 56 through 78 removed outlier: 3.615A pdb=" N VAL l 60 " --> pdb=" O ILE l 56 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY l 69 " --> pdb=" O ILE l 65 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL l 72 " --> pdb=" O TYR l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 122 removed outlier: 3.541A pdb=" N SER l 89 " --> pdb=" O THR l 85 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 126 No H-bonds generated for 'chain 'l' and resid 124 through 126' Processing helix chain 'l' and resid 127 through 153 removed outlier: 4.012A pdb=" N LEU l 133 " --> pdb=" O VAL l 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE l 137 " --> pdb=" O LEU l 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA l 138 " --> pdb=" O ILE l 134 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY l 142 " --> pdb=" O ALA l 138 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 25 removed outlier: 3.960A pdb=" N GLY m 15 " --> pdb=" O SER m 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA m 19 " --> pdb=" O GLY m 15 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET m 23 " --> pdb=" O ALA m 19 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE m 25 " --> pdb=" O SER m 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 46 removed outlier: 3.917A pdb=" N THR m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA m 43 " --> pdb=" O THR m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 47 through 52 removed outlier: 6.073A pdb=" N GLU m 50 " --> pdb=" O MET m 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU m 51 " --> pdb=" O ARG m 48 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE m 52 " --> pdb=" O PRO m 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 47 through 52' Processing helix chain 'm' and resid 53 through 55 No H-bonds generated for 'chain 'm' and resid 53 through 55' Processing helix chain 'm' and resid 56 through 78 removed outlier: 3.573A pdb=" N MET m 61 " --> pdb=" O ILE m 57 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA m 62 " --> pdb=" O PRO m 58 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA m 73 " --> pdb=" O GLY m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 122 removed outlier: 3.742A pdb=" N ARG m 119 " --> pdb=" O ASP m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 155 removed outlier: 4.542A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU m 133 " --> pdb=" O VAL m 129 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE m 134 " --> pdb=" O GLY m 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY m 142 " --> pdb=" O ALA m 138 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS m 155 " --> pdb=" O ILE m 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 24 removed outlier: 4.151A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 45 removed outlier: 5.119A pdb=" N SER n 37 " --> pdb=" O GLY n 33 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA n 43 " --> pdb=" O THR n 39 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 55 removed outlier: 3.614A pdb=" N LEU n 51 " --> pdb=" O ARG n 48 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET n 53 " --> pdb=" O GLU n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 80 removed outlier: 3.752A pdb=" N LEU n 80 " --> pdb=" O ILE n 76 " (cutoff:3.500A) Processing helix chain 'n' and resid 85 through 121 Processing helix chain 'n' and resid 122 through 125 Proline residue: n 125 - end of helix No H-bonds generated for 'chain 'n' and resid 122 through 125' Processing helix chain 'n' and resid 126 through 155 removed outlier: 4.280A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE n 137 " --> pdb=" O LEU n 133 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU n 141 " --> pdb=" O PHE n 137 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY n 142 " --> pdb=" O ALA n 138 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU n 143 " --> pdb=" O GLU n 139 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 45 removed outlier: 4.470A pdb=" N PHE o 14 " --> pdb=" O TYR o 10 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER o 26 " --> pdb=" O ALA o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 47 No H-bonds generated for 'chain 'o' and resid 46 through 47' Processing helix chain 'o' and resid 48 through 52 removed outlier: 3.757A pdb=" N ILE o 52 " --> pdb=" O PRO o 49 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 54 No H-bonds generated for 'chain 'o' and resid 53 through 54' Processing helix chain 'o' and resid 55 through 80 removed outlier: 4.590A pdb=" N VAL o 59 " --> pdb=" O SER o 55 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE o 65 " --> pdb=" O MET o 61 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA o 66 " --> pdb=" O ALA o 62 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU o 75 " --> pdb=" O VAL o 71 " (cutoff:3.500A) Processing helix chain 'o' and resid 85 through 124 removed outlier: 3.936A pdb=" N ARG o 119 " --> pdb=" O ASP o 115 " (cutoff:3.500A) Processing helix chain 'o' and resid 126 through 152 removed outlier: 4.529A pdb=" N GLY o 130 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU o 141 " --> pdb=" O PHE o 137 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY o 142 " --> pdb=" O ALA o 138 " (cutoff:3.500A) Processing helix chain 'p' and resid 600 through 628 removed outlier: 4.231A pdb=" N ASN p 606 " --> pdb=" O SER p 602 " (cutoff:3.500A) Processing helix chain 'e' and resid 6 through 27 Proline residue: e 25 - end of helix Processing helix chain 'e' and resid 33 through 58 removed outlier: 3.562A pdb=" N ILE e 37 " --> pdb=" O ASN e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 78 removed outlier: 3.776A pdb=" N ARG e 77 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 21 through 33 removed outlier: 3.600A pdb=" N CYS a 25 " --> pdb=" O ALA a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 75 Processing helix chain 'a' and resid 92 through 129 removed outlier: 3.725A pdb=" N ASP a 96 " --> pdb=" O ARG a 92 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA a 117 " --> pdb=" O THR a 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU a 118 " --> pdb=" O ASN a 114 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 191 Processing helix chain 'a' and resid 226 through 241 Processing helix chain 'a' and resid 251 through 274 removed outlier: 3.503A pdb=" N LYS a 255 " --> pdb=" O PRO a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 274 through 285 Processing helix chain 'a' and resid 287 through 309 removed outlier: 4.079A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP a 293 " --> pdb=" O ASN a 289 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU a 309 " --> pdb=" O HIS a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 314 through 318 Processing helix chain 'a' and resid 329 through 344 Processing helix chain 'a' and resid 371 through 380 removed outlier: 3.828A pdb=" N ILE a 377 " --> pdb=" O GLY a 373 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL a 378 " --> pdb=" O PHE a 374 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.805A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 409 through 426 Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 removed outlier: 3.972A pdb=" N GLY a 446 " --> pdb=" O MET a 442 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 464 Processing helix chain 'a' and resid 481 through 486 Processing helix chain 'a' and resid 487 through 489 No H-bonds generated for 'chain 'a' and resid 487 through 489' Processing helix chain 'a' and resid 492 through 500 removed outlier: 3.968A pdb=" N SER a 498 " --> pdb=" O LEU a 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL a 500 " --> pdb=" O GLY a 497 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 525 Processing helix chain 'a' and resid 528 through 563 removed outlier: 4.151A pdb=" N PHE a 532 " --> pdb=" O ASN a 528 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE a 563 " --> pdb=" O ASN a 559 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 572 Processing helix chain 'a' and resid 572 through 598 removed outlier: 3.550A pdb=" N GLU a 576 " --> pdb=" O GLY a 572 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR a 598 " --> pdb=" O LYS a 594 " (cutoff:3.500A) Processing helix chain 'a' and resid 608 through 619 removed outlier: 3.555A pdb=" N HIS a 612 " --> pdb=" O SER a 608 " (cutoff:3.500A) Processing helix chain 'a' and resid 632 through 651 removed outlier: 4.070A pdb=" N ILE a 636 " --> pdb=" O GLY a 632 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix Processing helix chain 'a' and resid 653 through 667 removed outlier: 3.553A pdb=" N LYS a 667 " --> pdb=" O TYR a 663 " (cutoff:3.500A) Processing helix chain 'a' and resid 713 through 739 removed outlier: 3.970A pdb=" N ILE a 733 " --> pdb=" O CYS a 729 " (cutoff:3.500A) Processing helix chain 'a' and resid 740 through 760 Processing helix chain 'a' and resid 771 through 790 removed outlier: 3.635A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 809 Processing helix chain 'a' and resid 811 through 815 removed outlier: 3.572A pdb=" N LYS a 814 " --> pdb=" O PHE a 811 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 252 through 255 removed outlier: 3.860A pdb=" N ILE c 261 " --> pdb=" O TYR c 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 276 through 278 Processing sheet with id=AA3, first strand: chain 'c' and resid 295 through 297 removed outlier: 5.692A pdb=" N ALA c 313 " --> pdb=" O PRO c 309 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA c 322 " --> pdb=" O MET c 336 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N MET c 336 " --> pdb=" O ALA c 322 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ARG c 324 " --> pdb=" O PHE c 334 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE c 334 " --> pdb=" O ARG c 324 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR c 326 " --> pdb=" O TYR c 332 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR c 332 " --> pdb=" O TYR c 326 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE c 334 " --> pdb=" O GLY c 357 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY c 357 " --> pdb=" O PHE c 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 36 through 38 removed outlier: 3.686A pdb=" N GLU a 322 " --> pdb=" O ARG a 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 171 through 176 Processing sheet with id=AA6, first strand: chain 'a' and resid 206 through 207 1688 hydrogen bonds defined for protein. 4935 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: 8.16 Time building geometry restraints manager: 10.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3919 1.33 - 1.45: 6347 1.45 - 1.57: 13480 1.57 - 1.70: 0 1.70 - 1.82: 284 Bond restraints: 24030 Sorted by residual: bond pdb=" C VAL a 553 " pdb=" O VAL a 553 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.19e-02 7.06e+03 1.56e+01 bond pdb=" N VAL a 553 " pdb=" CA VAL a 553 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.21e-02 6.83e+03 1.50e+01 bond pdb=" C ILE a 546 " pdb=" O ILE a 546 " ideal model delta sigma weight residual 1.237 1.280 -0.043 1.19e-02 7.06e+03 1.32e+01 bond pdb=" C MET a 549 " pdb=" O MET a 549 " ideal model delta sigma weight residual 1.237 1.280 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" N LEU a 557 " pdb=" CA LEU a 557 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.21e-02 6.83e+03 1.13e+01 ... (remaining 24025 not shown) Histogram of bond angle deviations from ideal: 96.14 - 103.75: 325 103.75 - 111.37: 10053 111.37 - 118.98: 9184 118.98 - 126.60: 12744 126.60 - 134.22: 266 Bond angle restraints: 32572 Sorted by residual: angle pdb=" C LEU a 557 " pdb=" N PHE a 558 " pdb=" CA PHE a 558 " ideal model delta sigma weight residual 120.44 127.78 -7.34 1.30e+00 5.92e-01 3.19e+01 angle pdb=" N LEU a 550 " pdb=" CA LEU a 550 " pdb=" C LEU a 550 " ideal model delta sigma weight residual 111.82 105.31 6.51 1.16e+00 7.43e-01 3.15e+01 angle pdb=" N LEU c 443 " pdb=" CA LEU c 443 " pdb=" CB LEU c 443 " ideal model delta sigma weight residual 110.46 118.93 -8.47 1.60e+00 3.91e-01 2.80e+01 angle pdb=" N PHE a 551 " pdb=" CA PHE a 551 " pdb=" C PHE a 551 " ideal model delta sigma weight residual 110.97 105.46 5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" CA LEU a 557 " pdb=" C LEU a 557 " pdb=" O LEU a 557 " ideal model delta sigma weight residual 120.55 115.19 5.36 1.06e+00 8.90e-01 2.56e+01 ... (remaining 32567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 12958 23.53 - 47.07: 1072 47.07 - 70.60: 118 70.60 - 94.14: 22 94.14 - 117.67: 3 Dihedral angle restraints: 14173 sinusoidal: 5481 harmonic: 8692 Sorted by residual: dihedral pdb=" CA ILE a 507 " pdb=" C ILE a 507 " pdb=" N PRO a 508 " pdb=" CA PRO a 508 " ideal model delta harmonic sigma weight residual 180.00 150.24 29.76 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLN c 266 " pdb=" C GLN c 266 " pdb=" N ASN c 267 " pdb=" CA ASN c 267 " ideal model delta harmonic sigma weight residual 180.00 155.08 24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA SER h 20 " pdb=" C SER h 20 " pdb=" N SER h 21 " pdb=" CA SER h 21 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 14170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 3825 0.156 - 0.311: 10 0.311 - 0.467: 0 0.467 - 0.622: 1 0.622 - 0.778: 1 Chirality restraints: 3837 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN c 267 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.09e+01 chirality pdb=" C1 NAG c 503 " pdb=" ND2 ASN c 297 " pdb=" C2 NAG c 503 " pdb=" O5 NAG c 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.83e+00 ... (remaining 3834 not shown) Planarity restraints: 4047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU a 557 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LEU a 557 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU a 557 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE a 558 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE a 507 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO a 508 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO a 508 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO a 508 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 459 " 0.019 2.00e-02 2.50e+03 1.91e-02 7.28e+00 pdb=" CG TYR a 459 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR a 459 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR a 459 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR a 459 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR a 459 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR a 459 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR a 459 " -0.004 2.00e-02 2.50e+03 ... (remaining 4044 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 10301 2.92 - 3.41: 25946 3.41 - 3.91: 37270 3.91 - 4.40: 42258 4.40 - 4.90: 67138 Nonbonded interactions: 182913 Sorted by model distance: nonbonded pdb=" O PHE c 415 " pdb=" OG SER c 416 " model vdw 2.423 2.440 nonbonded pdb=" OD1 ASN c 267 " pdb=" C1 NAG C 1 " model vdw 2.425 2.776 nonbonded pdb=" OG SER m 45 " pdb=" OE1 GLN n 124 " model vdw 2.476 2.440 nonbonded pdb=" O SER c 369 " pdb=" OG SER c 370 " model vdw 2.478 2.440 nonbonded pdb=" N LEU c 443 " pdb=" O LEU c 443 " model vdw 2.496 2.496 ... (remaining 182908 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 'B' selection = chain 'C' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } 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: 1.300 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: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 63.060 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.140 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 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 : 0.005 0.093 24030 Z= 0.303 Angle : 0.876 13.407 32572 Z= 0.473 Chirality : 0.045 0.778 3837 Planarity : 0.006 0.094 4040 Dihedral : 16.139 117.672 8643 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 2.88 % Allowed : 19.37 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3030 helix: 0.52 (0.11), residues: 2148 sheet: -0.86 (0.61), residues: 61 loop : -2.03 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 293 HIS 0.008 0.001 HIS c 364 PHE 0.030 0.002 PHE a 777 TYR 0.045 0.002 TYR a 459 ARG 0.012 0.001 ARG a 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 582 time to evaluate : 2.415 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: c 447 ASP cc_start: 0.7372 (t70) cc_final: 0.6431 (p0) REVERT: c 448 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7439 (ttm110) REVERT: c 449 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: d 87 MET cc_start: 0.7348 (mmt) cc_final: 0.7014 (tpp) REVERT: d 104 TYR cc_start: 0.6650 (m-10) cc_final: 0.6353 (m-10) REVERT: d 108 ILE cc_start: 0.7051 (mt) cc_final: 0.6803 (mt) REVERT: d 149 PRO cc_start: 0.7339 (Cg_endo) cc_final: 0.7091 (Cg_exo) REVERT: f 50 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7106 (t0) REVERT: f 61 LEU cc_start: 0.3834 (tp) cc_final: 0.2990 (tp) REVERT: g 10 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.5195 (m-80) REVERT: g 17 MET cc_start: 0.5953 (ttm) cc_final: 0.5593 (tpt) REVERT: h 41 ILE cc_start: 0.6458 (pt) cc_final: 0.6029 (tt) REVERT: h 110 ILE cc_start: 0.6365 (mt) cc_final: 0.6076 (pt) REVERT: h 128 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6446 (t80) REVERT: h 144 TYR cc_start: 0.6493 (m-10) cc_final: 0.5950 (m-10) REVERT: i 54 LYS cc_start: 0.7039 (mmtt) cc_final: 0.6530 (mmmt) REVERT: i 65 ILE cc_start: 0.7171 (tp) cc_final: 0.6874 (tp) REVERT: j 108 PHE cc_start: 0.4450 (OUTLIER) cc_final: 0.3972 (t80) REVERT: k 44 MET cc_start: 0.7675 (tmm) cc_final: 0.7148 (ppp) REVERT: k 108 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5916 (m-80) REVERT: l 23 MET cc_start: 0.6262 (tpt) cc_final: 0.6033 (tpt) REVERT: m 7 ASN cc_start: 0.6092 (m-40) cc_final: 0.5729 (p0) REVERT: m 24 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7569 (t) REVERT: m 155 LYS cc_start: 0.6679 (tptt) cc_final: 0.6347 (tptp) REVERT: n 61 MET cc_start: 0.6427 (mmt) cc_final: 0.6090 (mmt) REVERT: o 47 MET cc_start: 0.8346 (tmm) cc_final: 0.7989 (tmm) REVERT: a 59 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8427 (mt-10) REVERT: a 257 MET cc_start: 0.8107 (ptp) cc_final: 0.7781 (ptp) REVERT: a 338 ARG cc_start: 0.8752 (mmt180) cc_final: 0.8456 (mmt180) REVERT: a 395 THR cc_start: 0.7753 (m) cc_final: 0.7534 (p) REVERT: a 752 LEU cc_start: 0.7901 (mt) cc_final: 0.7575 (mt) REVERT: a 759 MET cc_start: 0.5863 (ptt) cc_final: 0.5005 (tmm) outliers start: 71 outliers final: 51 residues processed: 632 average time/residue: 0.3317 time to fit residues: 326.3181 Evaluate side-chains 557 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 499 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 323 SER Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 362 SER Chi-restraints excluded: chain c residue 372 SER Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 416 SER Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain d residue 25 LEU Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 321 VAL Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 50 ASP Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 11 SER Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain k residue 9 GLU Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 37 SER Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 377 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 643 VAL Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 726 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 276 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 348 ASN ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 92 GLN o 123 GLN ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24030 Z= 0.262 Angle : 0.706 9.401 32572 Z= 0.363 Chirality : 0.044 0.476 3837 Planarity : 0.005 0.060 4040 Dihedral : 8.758 113.138 3607 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 5.79 % Allowed : 18.72 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3030 helix: 1.28 (0.11), residues: 2109 sheet: -0.48 (0.59), residues: 68 loop : -1.82 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 40 HIS 0.012 0.001 HIS a 766 PHE 0.020 0.002 PHE g 128 TYR 0.033 0.002 TYR a 459 ARG 0.010 0.001 ARG a 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 542 time to evaluate : 2.482 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: c 447 ASP cc_start: 0.7417 (t70) cc_final: 0.6608 (p0) REVERT: c 448 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7448 (ttm110) REVERT: c 449 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.6727 (m-80) REVERT: b 204 MET cc_start: 0.7512 (ttp) cc_final: 0.7305 (ttm) REVERT: d 87 MET cc_start: 0.7644 (mmt) cc_final: 0.7436 (tpp) REVERT: d 139 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6428 (pm20) REVERT: d 191 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.6394 (t80) REVERT: f 61 LEU cc_start: 0.3637 (tp) cc_final: 0.3371 (tp) REVERT: g 17 MET cc_start: 0.6255 (ttm) cc_final: 0.6019 (tpt) REVERT: h 41 ILE cc_start: 0.5946 (pt) cc_final: 0.5664 (tt) REVERT: h 110 ILE cc_start: 0.6467 (mt) cc_final: 0.6086 (pt) REVERT: h 128 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6282 (t80) REVERT: h 136 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7703 (tt) REVERT: i 54 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6415 (mmmt) REVERT: j 44 MET cc_start: 0.6506 (tmm) cc_final: 0.6256 (tmm) REVERT: j 108 PHE cc_start: 0.4596 (OUTLIER) cc_final: 0.4221 (m-80) REVERT: j 133 LEU cc_start: 0.5375 (tp) cc_final: 0.5146 (tt) REVERT: k 44 MET cc_start: 0.7685 (tmm) cc_final: 0.7268 (ppp) REVERT: k 57 ILE cc_start: 0.8111 (mm) cc_final: 0.7907 (mp) REVERT: k 108 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: n 61 MET cc_start: 0.6208 (mmt) cc_final: 0.5820 (mmt) REVERT: o 47 MET cc_start: 0.8330 (tmm) cc_final: 0.7860 (tmm) REVERT: a 11 THR cc_start: 0.4828 (OUTLIER) cc_final: 0.4493 (p) REVERT: a 74 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8695 (pttp) REVERT: a 188 TRP cc_start: 0.7909 (t60) cc_final: 0.7495 (t-100) REVERT: a 298 ARG cc_start: 0.8264 (tpp80) cc_final: 0.7979 (mmt90) REVERT: a 354 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7820 (ttm170) REVERT: a 398 THR cc_start: 0.8668 (t) cc_final: 0.8441 (m) REVERT: a 399 PHE cc_start: 0.7239 (t80) cc_final: 0.6943 (t80) REVERT: a 406 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8010 (mtp) REVERT: a 453 MET cc_start: 0.8380 (mtp) cc_final: 0.8148 (mtp) REVERT: a 752 LEU cc_start: 0.7931 (mt) cc_final: 0.7669 (mt) REVERT: a 759 MET cc_start: 0.6615 (ptt) cc_final: 0.5570 (tmm) outliers start: 143 outliers final: 90 residues processed: 629 average time/residue: 0.3305 time to fit residues: 330.7774 Evaluate side-chains 582 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 483 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 135 LEU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 569 ILE Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 658 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 298 optimal weight: 0.1980 chunk 246 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 342 HIS ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 278 HIS ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24030 Z= 0.311 Angle : 0.714 9.750 32572 Z= 0.368 Chirality : 0.044 0.462 3837 Planarity : 0.005 0.066 4040 Dihedral : 8.344 109.806 3545 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 7.86 % Allowed : 20.02 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3030 helix: 1.16 (0.11), residues: 2119 sheet: -0.68 (0.59), residues: 68 loop : -1.98 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 333 HIS 0.011 0.001 HIS a 766 PHE 0.025 0.002 PHE a 67 TYR 0.021 0.002 TYR b 71 ARG 0.013 0.001 ARG d 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 510 time to evaluate : 2.505 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: c 449 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.6918 (m-80) REVERT: d 108 ILE cc_start: 0.7308 (mt) cc_final: 0.7002 (mp) REVERT: d 191 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.6444 (t80) REVERT: f 25 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6836 (ttt) REVERT: h 110 ILE cc_start: 0.6495 (mt) cc_final: 0.6031 (pt) REVERT: h 128 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6178 (t80) REVERT: h 136 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7842 (tt) REVERT: i 54 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6453 (mmmt) REVERT: j 44 MET cc_start: 0.6183 (tmm) cc_final: 0.5765 (tmm) REVERT: j 108 PHE cc_start: 0.4679 (OUTLIER) cc_final: 0.4243 (m-80) REVERT: k 44 MET cc_start: 0.7656 (tmm) cc_final: 0.7283 (ppp) REVERT: k 108 PHE cc_start: 0.6373 (OUTLIER) cc_final: 0.6133 (m-80) REVERT: n 17 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6942 (ttp) REVERT: o 47 MET cc_start: 0.8337 (tmm) cc_final: 0.7838 (tmm) REVERT: a 74 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8622 (pttm) REVERT: a 188 TRP cc_start: 0.8152 (t60) cc_final: 0.7880 (t-100) REVERT: a 277 ASP cc_start: 0.8208 (m-30) cc_final: 0.7731 (t0) REVERT: a 403 PHE cc_start: 0.8447 (t80) cc_final: 0.8117 (t80) REVERT: a 406 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8040 (mtp) REVERT: a 453 MET cc_start: 0.8316 (mtp) cc_final: 0.8014 (mtp) REVERT: a 467 CYS cc_start: 0.6583 (t) cc_final: 0.5998 (m) REVERT: a 752 LEU cc_start: 0.7946 (mt) cc_final: 0.7674 (mt) REVERT: a 759 MET cc_start: 0.6778 (ptt) cc_final: 0.5422 (tmm) outliers start: 194 outliers final: 132 residues processed: 636 average time/residue: 0.3160 time to fit residues: 319.8471 Evaluate side-chains 612 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 471 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 316 VAL Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 113 VAL Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 136 ILE Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 44 MET Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain a residue 76 ASN Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 569 ILE Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 620 SER Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 658 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 4.9990 chunk 207 optimal weight: 0.0970 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 376 ASN d 342 HIS ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 ASN ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24030 Z= 0.277 Angle : 0.694 9.654 32572 Z= 0.355 Chirality : 0.043 0.459 3837 Planarity : 0.005 0.067 4040 Dihedral : 8.268 106.338 3544 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 8.79 % Allowed : 20.79 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3030 helix: 1.18 (0.11), residues: 2133 sheet: -0.06 (0.76), residues: 42 loop : -2.08 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP a 293 HIS 0.005 0.001 HIS a 766 PHE 0.022 0.002 PHE a 475 TYR 0.018 0.002 TYR b 71 ARG 0.008 0.001 ARG a 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 508 time to evaluate : 2.400 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: c 449 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: b 92 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5733 (mp) REVERT: d 191 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.6436 (t80) REVERT: f 25 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6826 (ttt) REVERT: g 10 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.5367 (m-80) REVERT: h 23 MET cc_start: 0.5279 (tpt) cc_final: 0.5029 (tpt) REVERT: h 44 MET cc_start: 0.5636 (ptp) cc_final: 0.5294 (ptp) REVERT: h 110 ILE cc_start: 0.6333 (mt) cc_final: 0.5926 (pt) REVERT: h 128 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6038 (t80) REVERT: h 136 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7875 (tt) REVERT: i 47 MET cc_start: 0.4993 (mtp) cc_final: 0.4773 (mtp) REVERT: i 54 LYS cc_start: 0.6985 (mmtt) cc_final: 0.6443 (mmmt) REVERT: j 108 PHE cc_start: 0.4799 (OUTLIER) cc_final: 0.4374 (m-80) REVERT: k 108 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: l 17 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.5590 (ttp) REVERT: n 17 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6972 (ttp) REVERT: o 47 MET cc_start: 0.8335 (tmm) cc_final: 0.7793 (tmm) REVERT: e 59 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: e 63 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7328 (mm) REVERT: a 74 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8589 (pttm) REVERT: a 101 PHE cc_start: 0.6467 (m-10) cc_final: 0.5988 (m-10) REVERT: a 277 ASP cc_start: 0.8219 (m-30) cc_final: 0.7681 (t0) REVERT: a 354 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7815 (ttm170) REVERT: a 406 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8019 (mtp) REVERT: a 467 CYS cc_start: 0.6514 (t) cc_final: 0.5984 (m) REVERT: a 580 MET cc_start: 0.7728 (tpp) cc_final: 0.7124 (tpp) REVERT: a 752 LEU cc_start: 0.7990 (mt) cc_final: 0.7707 (mt) REVERT: a 759 MET cc_start: 0.6708 (ptt) cc_final: 0.5396 (tmm) outliers start: 217 outliers final: 153 residues processed: 650 average time/residue: 0.3223 time to fit residues: 332.0444 Evaluate side-chains 631 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 464 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 447 ASP Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 92 LEU Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 53 MET Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 52 ILE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 44 MET Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 76 ASN Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 569 ILE Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 648 VAL Chi-restraints excluded: chain a residue 657 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 717 THR Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 364 HIS c 392 ASN ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 ASN a 48 GLN a 473 ASN ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24030 Z= 0.407 Angle : 0.818 11.791 32572 Z= 0.421 Chirality : 0.047 0.507 3837 Planarity : 0.005 0.072 4040 Dihedral : 8.576 104.697 3544 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 10.66 % Allowed : 20.42 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3030 helix: 0.68 (0.11), residues: 2140 sheet: -0.80 (0.60), residues: 66 loop : -2.32 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP a 293 HIS 0.006 0.001 HIS a 766 PHE 0.027 0.003 PHE a 536 TYR 0.024 0.002 TYR b 71 ARG 0.011 0.001 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 479 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 437 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8948 (tp) REVERT: c 449 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: d 34 ASP cc_start: 0.7935 (m-30) cc_final: 0.7295 (m-30) REVERT: d 101 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.5855 (t80) REVERT: d 108 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6933 (mp) REVERT: d 191 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.6551 (t80) REVERT: f 25 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7017 (ttt) REVERT: g 10 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: g 112 ILE cc_start: 0.5700 (OUTLIER) cc_final: 0.5473 (mp) REVERT: g 139 GLU cc_start: 0.6571 (tm-30) cc_final: 0.6305 (tm-30) REVERT: h 110 ILE cc_start: 0.6275 (mt) cc_final: 0.5868 (pt) REVERT: h 136 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7923 (tt) REVERT: i 54 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6534 (mmmt) REVERT: i 87 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.5332 (t80) REVERT: j 9 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5913 (mm-30) REVERT: j 44 MET cc_start: 0.6402 (tmm) cc_final: 0.6121 (tmm) REVERT: j 108 PHE cc_start: 0.4580 (OUTLIER) cc_final: 0.4068 (m-80) REVERT: k 44 MET cc_start: 0.8212 (tmm) cc_final: 0.7043 (ppp) REVERT: k 108 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: l 17 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.5800 (ttp) REVERT: m 61 MET cc_start: 0.6860 (mmt) cc_final: 0.6386 (mmt) REVERT: n 17 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7042 (ttp) REVERT: o 47 MET cc_start: 0.8301 (tmm) cc_final: 0.7735 (tmm) REVERT: p 630 ASP cc_start: 0.8309 (t0) cc_final: 0.8092 (t0) REVERT: e 63 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7380 (mm) REVERT: a 62 ASP cc_start: 0.8234 (m-30) cc_final: 0.7888 (m-30) REVERT: a 74 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8651 (pttp) REVERT: a 101 PHE cc_start: 0.6461 (m-10) cc_final: 0.5869 (m-10) REVERT: a 291 ARG cc_start: 0.7095 (mmp80) cc_final: 0.6790 (mmp80) REVERT: a 354 ARG cc_start: 0.8069 (ttm170) cc_final: 0.7854 (ttm170) REVERT: a 406 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: a 467 CYS cc_start: 0.6749 (t) cc_final: 0.6054 (m) REVERT: a 475 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6584 (p90) REVERT: a 752 LEU cc_start: 0.8016 (mt) cc_final: 0.7720 (mt) REVERT: a 759 MET cc_start: 0.6723 (ptt) cc_final: 0.5434 (tmm) REVERT: a 786 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7321 (tp) outliers start: 263 outliers final: 196 residues processed: 656 average time/residue: 0.3108 time to fit residues: 327.5161 Evaluate side-chains 666 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 452 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 270 VAL Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain c residue 447 ASP Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 101 PHE Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 205 THR Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 316 VAL Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 65 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 113 VAL Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain h residue 137 PHE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 87 TYR Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 136 ILE Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 146 LEU Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 47 MET Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 44 MET Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 136 ILE Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 71 VAL Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 7 ASN Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 76 ASN Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 475 PHE Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 569 ILE Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 648 VAL Chi-restraints excluded: chain a residue 657 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 726 ILE Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 786 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 9.9990 chunk 264 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 ASN a 48 GLN a 112 ASN a 524 ASN a 766 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24030 Z= 0.239 Angle : 0.700 9.556 32572 Z= 0.355 Chirality : 0.043 0.449 3837 Planarity : 0.005 0.066 4040 Dihedral : 8.473 119.003 3542 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 7.86 % Allowed : 23.95 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3030 helix: 1.14 (0.11), residues: 2122 sheet: 0.20 (0.80), residues: 40 loop : -2.18 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP a 293 HIS 0.006 0.001 HIS a 766 PHE 0.028 0.002 PHE o 90 TYR 0.025 0.002 TYR d 153 ARG 0.007 0.001 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 492 time to evaluate : 2.641 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: c 449 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6731 (m-80) REVERT: b 68 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.8094 (t60) REVERT: d 101 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.6076 (t80) REVERT: d 108 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6952 (mp) REVERT: d 191 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.6495 (t80) REVERT: f 25 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6852 (ttt) REVERT: g 10 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5479 (m-80) REVERT: g 112 ILE cc_start: 0.5491 (OUTLIER) cc_final: 0.5280 (mp) REVERT: g 139 GLU cc_start: 0.6439 (tm-30) cc_final: 0.6105 (tm-30) REVERT: h 110 ILE cc_start: 0.6375 (mt) cc_final: 0.5943 (pt) REVERT: h 136 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7962 (tt) REVERT: i 47 MET cc_start: 0.4756 (mtp) cc_final: 0.4472 (mtp) REVERT: i 54 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6569 (mmmt) REVERT: j 108 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4574 (m-80) REVERT: k 44 MET cc_start: 0.8138 (tmm) cc_final: 0.7002 (ppp) REVERT: k 108 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: l 17 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5612 (ttp) REVERT: m 61 MET cc_start: 0.6848 (mmt) cc_final: 0.6402 (mmt) REVERT: n 17 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6798 (ttp) REVERT: o 47 MET cc_start: 0.8319 (tmm) cc_final: 0.7741 (tmm) REVERT: o 131 MET cc_start: 0.6395 (ttp) cc_final: 0.6141 (tmm) REVERT: p 630 ASP cc_start: 0.8424 (t0) cc_final: 0.8168 (t0) REVERT: a 74 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8654 (pttp) REVERT: a 277 ASP cc_start: 0.8106 (m-30) cc_final: 0.7401 (t0) REVERT: a 293 TRP cc_start: 0.5610 (OUTLIER) cc_final: 0.5278 (t60) REVERT: a 398 THR cc_start: 0.8710 (t) cc_final: 0.8347 (m) REVERT: a 406 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7965 (mtp) REVERT: a 453 MET cc_start: 0.8176 (mtp) cc_final: 0.7680 (mtp) REVERT: a 467 CYS cc_start: 0.6579 (t) cc_final: 0.6001 (m) REVERT: a 571 PHE cc_start: 0.7279 (m-80) cc_final: 0.6991 (m-80) REVERT: a 580 MET cc_start: 0.8057 (tpp) cc_final: 0.7607 (tpp) REVERT: a 665 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7572 (mmm160) REVERT: a 752 LEU cc_start: 0.7818 (mt) cc_final: 0.7548 (mt) REVERT: a 759 MET cc_start: 0.6655 (ptt) cc_final: 0.5441 (tmm) outliers start: 194 outliers final: 139 residues processed: 623 average time/residue: 0.3117 time to fit residues: 311.5273 Evaluate side-chains 614 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 460 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 447 ASP Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 101 PHE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 205 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 146 LEU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 293 TRP Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 569 ILE Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 657 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 717 THR Chi-restraints excluded: chain a residue 763 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 293 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 349 HIS ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 ASN ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 45 ASN a 48 GLN ** a 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 749 HIS a 766 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24030 Z= 0.252 Angle : 0.702 9.851 32572 Z= 0.355 Chirality : 0.043 0.457 3837 Planarity : 0.005 0.067 4040 Dihedral : 8.335 122.210 3542 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 8.06 % Allowed : 25.00 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3030 helix: 1.19 (0.11), residues: 2124 sheet: 0.11 (0.79), residues: 40 loop : -2.17 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP a 293 HIS 0.006 0.001 HIS a 766 PHE 0.027 0.002 PHE b 174 TYR 0.018 0.002 TYR a 562 ARG 0.008 0.001 ARG l 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 471 time to evaluate : 2.295 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: c 449 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.6784 (m-80) REVERT: b 92 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5883 (mp) REVERT: d 101 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.5843 (t80) REVERT: d 104 TYR cc_start: 0.6656 (m-80) cc_final: 0.6355 (m-80) REVERT: d 108 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.7001 (mp) REVERT: d 191 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.6474 (t80) REVERT: f 25 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6728 (ttt) REVERT: g 10 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: g 112 ILE cc_start: 0.5481 (OUTLIER) cc_final: 0.5252 (mp) REVERT: g 123 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.5600 (mp10) REVERT: g 139 GLU cc_start: 0.6357 (tm-30) cc_final: 0.6048 (tm-30) REVERT: h 110 ILE cc_start: 0.6356 (mt) cc_final: 0.5883 (pt) REVERT: i 54 LYS cc_start: 0.7010 (mmtt) cc_final: 0.6563 (mmmt) REVERT: j 17 MET cc_start: 0.7377 (ttt) cc_final: 0.7073 (ttm) REVERT: j 108 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: k 44 MET cc_start: 0.8136 (tmm) cc_final: 0.7078 (ppp) REVERT: k 108 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: l 17 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.5685 (ttp) REVERT: l 124 GLN cc_start: 0.7254 (tp-100) cc_final: 0.5809 (tm-30) REVERT: m 61 MET cc_start: 0.6921 (mmt) cc_final: 0.6448 (mmt) REVERT: n 17 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7121 (tmm) REVERT: o 47 MET cc_start: 0.8273 (tmm) cc_final: 0.7658 (tmm) REVERT: p 630 ASP cc_start: 0.8443 (t0) cc_final: 0.8218 (t0) REVERT: a 74 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8704 (pttp) REVERT: a 293 TRP cc_start: 0.6121 (OUTLIER) cc_final: 0.5834 (t60) REVERT: a 398 THR cc_start: 0.8718 (t) cc_final: 0.8344 (m) REVERT: a 406 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7969 (mtp) REVERT: a 453 MET cc_start: 0.8195 (mtp) cc_final: 0.7878 (mtp) REVERT: a 467 CYS cc_start: 0.6570 (t) cc_final: 0.6028 (m) REVERT: a 571 PHE cc_start: 0.7316 (m-80) cc_final: 0.7033 (m-80) REVERT: a 580 MET cc_start: 0.8082 (tpp) cc_final: 0.7645 (tpp) REVERT: a 665 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7522 (mmm160) REVERT: a 713 ASP cc_start: 0.7167 (t0) cc_final: 0.6833 (p0) REVERT: a 752 LEU cc_start: 0.7819 (mt) cc_final: 0.7552 (mt) REVERT: a 759 MET cc_start: 0.6731 (ptt) cc_final: 0.5502 (tmm) outliers start: 199 outliers final: 158 residues processed: 604 average time/residue: 0.3164 time to fit residues: 306.4985 Evaluate side-chains 628 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 455 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 92 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 101 PHE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 205 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 53 MET Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 146 LEU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 124 GLN Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain k residue 151 ILE Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 47 MET Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 7 ASN Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 293 TRP Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 569 ILE Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 648 VAL Chi-restraints excluded: chain a residue 657 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 717 THR Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 791 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 392 ASN ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN o 123 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 24030 Z= 0.221 Angle : 0.690 10.697 32572 Z= 0.345 Chirality : 0.042 0.414 3837 Planarity : 0.004 0.066 4040 Dihedral : 8.070 121.689 3541 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 6.60 % Allowed : 26.82 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3030 helix: 1.35 (0.11), residues: 2132 sheet: -0.01 (0.77), residues: 42 loop : -2.24 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP a 293 HIS 0.008 0.001 HIS a 766 PHE 0.029 0.001 PHE b 174 TYR 0.019 0.001 TYR a 23 ARG 0.013 0.001 ARG l 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 471 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 447 ASP cc_start: 0.7632 (t70) cc_final: 0.6717 (p0) REVERT: c 449 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: b 68 TRP cc_start: 0.8560 (OUTLIER) cc_final: 0.8083 (t60) REVERT: d 107 MET cc_start: 0.6451 (mtp) cc_final: 0.5513 (mtp) REVERT: d 191 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.6429 (t80) REVERT: g 10 TYR cc_start: 0.6235 (OUTLIER) cc_final: 0.5275 (m-80) REVERT: g 112 ILE cc_start: 0.5493 (OUTLIER) cc_final: 0.5234 (mp) REVERT: g 123 GLN cc_start: 0.6630 (OUTLIER) cc_final: 0.5459 (mp10) REVERT: h 41 ILE cc_start: 0.5697 (pt) cc_final: 0.5477 (tt) REVERT: h 44 MET cc_start: 0.5706 (ptp) cc_final: 0.5381 (ptp) REVERT: h 110 ILE cc_start: 0.6319 (mt) cc_final: 0.5884 (pt) REVERT: i 54 LYS cc_start: 0.6958 (mmtt) cc_final: 0.6533 (mmmt) REVERT: i 139 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6534 (tm-30) REVERT: j 17 MET cc_start: 0.7367 (ttt) cc_final: 0.7093 (ttm) REVERT: j 108 PHE cc_start: 0.5157 (OUTLIER) cc_final: 0.4782 (m-80) REVERT: k 44 MET cc_start: 0.8126 (tmm) cc_final: 0.7078 (ppp) REVERT: k 108 PHE cc_start: 0.6339 (OUTLIER) cc_final: 0.6020 (m-80) REVERT: l 17 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.5538 (ttp) REVERT: m 61 MET cc_start: 0.6952 (mmt) cc_final: 0.6525 (mmt) REVERT: o 47 MET cc_start: 0.8298 (tmm) cc_final: 0.7668 (tmm) REVERT: o 126 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7676 (ttm170) REVERT: p 630 ASP cc_start: 0.8415 (t0) cc_final: 0.8199 (t0) REVERT: e 63 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7312 (mm) REVERT: a 71 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: a 74 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8705 (pttp) REVERT: a 293 TRP cc_start: 0.6463 (OUTLIER) cc_final: 0.6219 (t60) REVERT: a 398 THR cc_start: 0.8701 (t) cc_final: 0.8339 (m) REVERT: a 406 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7922 (mtp) REVERT: a 453 MET cc_start: 0.8172 (mtp) cc_final: 0.7836 (mtp) REVERT: a 467 CYS cc_start: 0.6550 (t) cc_final: 0.6087 (m) REVERT: a 571 PHE cc_start: 0.7279 (m-80) cc_final: 0.7068 (m-80) REVERT: a 580 MET cc_start: 0.8103 (tpp) cc_final: 0.7737 (tpp) REVERT: a 752 LEU cc_start: 0.7812 (mt) cc_final: 0.7534 (mt) REVERT: a 759 MET cc_start: 0.6722 (ptt) cc_final: 0.5595 (tmm) outliers start: 163 outliers final: 127 residues processed: 579 average time/residue: 0.3091 time to fit residues: 287.3558 Evaluate side-chains 599 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 458 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 205 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 53 MET Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 146 LEU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 293 TRP Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 648 VAL Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 717 THR Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 791 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 273 optimal weight: 0.0570 chunk 164 optimal weight: 8.9990 chunk 118 optimal weight: 0.5980 chunk 214 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 376 ASN ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 ASN ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN o 123 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 749 HIS a 766 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 24030 Z= 0.252 Angle : 0.719 14.757 32572 Z= 0.360 Chirality : 0.043 0.422 3837 Planarity : 0.005 0.079 4040 Dihedral : 8.017 121.302 3541 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 7.13 % Allowed : 26.13 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3030 helix: 1.27 (0.11), residues: 2132 sheet: -0.74 (0.68), residues: 57 loop : -2.25 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 293 HIS 0.008 0.001 HIS a 766 PHE 0.028 0.002 PHE b 174 TYR 0.015 0.002 TYR o 32 ARG 0.021 0.001 ARG l 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 457 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 447 ASP cc_start: 0.7680 (t70) cc_final: 0.6712 (p0) REVERT: c 449 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: b 68 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.8115 (t60) REVERT: d 80 MET cc_start: 0.8199 (tmm) cc_final: 0.7869 (ttt) REVERT: d 101 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.5761 (t80) REVERT: d 107 MET cc_start: 0.6444 (mtp) cc_final: 0.5549 (mtp) REVERT: d 191 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.6401 (t80) REVERT: g 10 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5334 (m-80) REVERT: g 112 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.5203 (mp) REVERT: h 110 ILE cc_start: 0.6359 (mt) cc_final: 0.5908 (pt) REVERT: i 54 LYS cc_start: 0.7064 (mmtt) cc_final: 0.6643 (mmmt) REVERT: i 139 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: j 108 PHE cc_start: 0.5135 (OUTLIER) cc_final: 0.4783 (m-80) REVERT: k 44 MET cc_start: 0.8125 (tmm) cc_final: 0.7089 (ppp) REVERT: k 108 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: l 17 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.5635 (ttp) REVERT: m 61 MET cc_start: 0.6947 (mmt) cc_final: 0.6535 (mmt) REVERT: o 47 MET cc_start: 0.8291 (tmm) cc_final: 0.7881 (tmm) REVERT: p 630 ASP cc_start: 0.8433 (t0) cc_final: 0.8218 (t0) REVERT: e 63 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7280 (mm) REVERT: a 59 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8796 (mm-30) REVERT: a 62 ASP cc_start: 0.8385 (m-30) cc_final: 0.8024 (m-30) REVERT: a 74 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8688 (pttm) REVERT: a 293 TRP cc_start: 0.6458 (OUTLIER) cc_final: 0.6222 (t60) REVERT: a 398 THR cc_start: 0.8733 (t) cc_final: 0.8367 (m) REVERT: a 406 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: a 453 MET cc_start: 0.8190 (mtp) cc_final: 0.7912 (mtp) REVERT: a 467 CYS cc_start: 0.6655 (t) cc_final: 0.6102 (m) REVERT: a 571 PHE cc_start: 0.7276 (m-80) cc_final: 0.7056 (m-80) REVERT: a 580 MET cc_start: 0.8136 (tpp) cc_final: 0.7775 (tpp) REVERT: a 713 ASP cc_start: 0.7209 (t0) cc_final: 0.6618 (p0) REVERT: a 752 LEU cc_start: 0.7837 (mt) cc_final: 0.7548 (mp) REVERT: a 759 MET cc_start: 0.6698 (ptt) cc_final: 0.5656 (tmm) outliers start: 176 outliers final: 149 residues processed: 583 average time/residue: 0.3139 time to fit residues: 294.6771 Evaluate side-chains 610 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 448 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 101 PHE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 205 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 57 ASN Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 53 MET Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 89 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 146 LEU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain k residue 151 ILE Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 135 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 7 ASN Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 607 LEU Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 293 TRP Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 567 LEU Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 648 VAL Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 717 THR Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 791 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 2.9990 chunk 288 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24030 Z= 0.251 Angle : 0.730 16.843 32572 Z= 0.362 Chirality : 0.043 0.408 3837 Planarity : 0.005 0.075 4040 Dihedral : 7.954 121.012 3541 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 6.73 % Allowed : 26.54 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3030 helix: 1.26 (0.11), residues: 2138 sheet: -0.72 (0.69), residues: 57 loop : -2.26 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 293 HIS 0.008 0.001 HIS a 766 PHE 0.028 0.002 PHE b 174 TYR 0.016 0.002 TYR j 10 ARG 0.020 0.001 ARG l 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 457 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 447 ASP cc_start: 0.7677 (t70) cc_final: 0.6716 (p0) REVERT: c 449 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: b 68 TRP cc_start: 0.8570 (OUTLIER) cc_final: 0.8147 (t60) REVERT: d 191 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.6405 (t80) REVERT: g 10 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5363 (m-80) REVERT: g 112 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.5308 (mp) REVERT: g 123 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.5540 (mp10) REVERT: h 110 ILE cc_start: 0.6368 (mt) cc_final: 0.5919 (pt) REVERT: i 54 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6638 (mmmt) REVERT: i 139 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: j 17 MET cc_start: 0.7334 (ttt) cc_final: 0.7065 (ttm) REVERT: j 108 PHE cc_start: 0.5123 (OUTLIER) cc_final: 0.4754 (m-80) REVERT: k 44 MET cc_start: 0.8067 (tmm) cc_final: 0.7073 (ppp) REVERT: k 108 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5997 (m-80) REVERT: l 17 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.5675 (ptm) REVERT: m 61 MET cc_start: 0.6839 (mmt) cc_final: 0.6429 (mmt) REVERT: o 47 MET cc_start: 0.8254 (tmm) cc_final: 0.7845 (tmm) REVERT: e 63 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7275 (mm) REVERT: a 59 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8780 (mm-30) REVERT: a 62 ASP cc_start: 0.8472 (m-30) cc_final: 0.8093 (m-30) REVERT: a 74 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8700 (pttm) REVERT: a 293 TRP cc_start: 0.6433 (OUTLIER) cc_final: 0.6202 (t60) REVERT: a 398 THR cc_start: 0.8732 (t) cc_final: 0.8363 (m) REVERT: a 406 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: a 453 MET cc_start: 0.8189 (mtp) cc_final: 0.7855 (mtp) REVERT: a 467 CYS cc_start: 0.6886 (t) cc_final: 0.6277 (m) REVERT: a 571 PHE cc_start: 0.7305 (m-80) cc_final: 0.7080 (m-80) REVERT: a 580 MET cc_start: 0.8136 (tpp) cc_final: 0.7778 (tpp) REVERT: a 713 ASP cc_start: 0.7318 (t0) cc_final: 0.6688 (p0) REVERT: a 752 LEU cc_start: 0.7825 (mt) cc_final: 0.7527 (mp) REVERT: a 759 MET cc_start: 0.6715 (ptt) cc_final: 0.5636 (tmm) outliers start: 166 outliers final: 147 residues processed: 576 average time/residue: 0.3080 time to fit residues: 285.4877 Evaluate side-chains 603 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 443 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 205 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 57 ASN Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 53 MET Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 89 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 146 LEU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 124 GLN Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain k residue 151 ILE Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 85 THR Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 135 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 81 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 7 ASN Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 607 LEU Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 293 TRP Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 368 ASN Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 567 LEU Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 648 VAL Chi-restraints excluded: chain a residue 657 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 717 THR Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 791 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.8980 chunk 256 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 222 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 129 HIS ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 GLN j 124 GLN o 123 GLN ** a 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 749 HIS a 766 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.162151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.137216 restraints weight = 44417.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.140768 restraints weight = 20938.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.143039 restraints weight = 12398.856| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24030 Z= 0.230 Angle : 0.718 15.011 32572 Z= 0.356 Chirality : 0.043 0.416 3837 Planarity : 0.005 0.080 4040 Dihedral : 7.855 120.908 3540 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 6.40 % Allowed : 27.11 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 3030 helix: 1.32 (0.11), residues: 2141 sheet: -0.71 (0.70), residues: 57 loop : -2.25 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP a 757 HIS 0.009 0.001 HIS a 766 PHE 0.029 0.002 PHE b 174 TYR 0.016 0.001 TYR a 23 ARG 0.021 0.001 ARG l 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5503.88 seconds wall clock time: 98 minutes 25.08 seconds (5905.08 seconds total)