Starting phenix.real_space_refine on Thu Aug 8 13:35:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/08_2024/9bry_44845.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/08_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_44845/08_2024/9bry_44845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/08_2024/9bry_44845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/08_2024/9bry_44845.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bry_44845/08_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-5409/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: 13.21, per 1000 atoms: 0.56 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: 9.58 Conformation dependent library (CDL) restraints added in 4.2 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: 2.24 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: 7.24 Time building geometry restraints manager: 10.44 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 3.040 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 3.040 nonbonded pdb=" O SER c 369 " pdb=" OG SER c 370 " model vdw 2.478 3.040 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 Time spend for trying shortcut: 0.00 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: 1.320 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: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 60.960 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.100 ------------------------------------------------------------------------------- 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 : 2.520 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: 0.3355 time to fit residues: 331.1663 Evaluate side-chains 557 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 499 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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: 9.9990 chunk 230 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** 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: 0.6630 moved from start: 0.1592 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= 0.281 Angle : 0.720 9.494 32572 Z= 0.371 Chirality : 0.045 0.493 3837 Planarity : 0.005 0.060 4040 Dihedral : 8.846 113.827 3607 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 5.63 % Allowed : 18.80 % Favored : 75.57 % 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: 0.51 (0.15), residues: 3030 helix: 1.23 (0.11), residues: 2109 sheet: -0.57 (0.58), residues: 68 loop : -1.83 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 293 HIS 0.016 0.001 HIS a 766 PHE 0.020 0.002 PHE g 128 TYR 0.032 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 673 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 534 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 447 ASP cc_start: 0.7348 (t70) cc_final: 0.6551 (p0) REVERT: c 448 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7458 (ttm110) REVERT: c 449 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: b 204 MET cc_start: 0.7532 (ttp) cc_final: 0.7313 (ttm) REVERT: d 87 MET cc_start: 0.7612 (mmt) cc_final: 0.7372 (tpp) REVERT: d 139 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6406 (pm20) REVERT: d 191 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.6400 (t80) REVERT: d 324 LYS cc_start: 0.7868 (ttmm) cc_final: 0.7205 (tttp) REVERT: g 17 MET cc_start: 0.6311 (ttm) cc_final: 0.6022 (tpt) REVERT: h 41 ILE cc_start: 0.6003 (pt) cc_final: 0.5653 (tt) REVERT: h 110 ILE cc_start: 0.6431 (mt) cc_final: 0.6050 (pt) REVERT: h 128 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6353 (t80) REVERT: h 136 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7702 (tt) REVERT: i 54 LYS cc_start: 0.7079 (mmtt) cc_final: 0.6425 (mmmt) REVERT: j 44 MET cc_start: 0.6508 (tmm) cc_final: 0.6228 (tmm) REVERT: j 108 PHE cc_start: 0.4566 (OUTLIER) cc_final: 0.4112 (m-80) REVERT: j 133 LEU cc_start: 0.5404 (tp) cc_final: 0.5177 (tt) REVERT: k 44 MET cc_start: 0.7714 (tmm) cc_final: 0.7264 (ppp) REVERT: k 57 ILE cc_start: 0.8128 (mm) cc_final: 0.7921 (mp) REVERT: k 108 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: l 47 MET cc_start: 0.7121 (pmm) cc_final: 0.6230 (pmm) REVERT: o 47 MET cc_start: 0.8330 (tmm) cc_final: 0.7859 (tmm) REVERT: a 11 THR cc_start: 0.4918 (OUTLIER) cc_final: 0.4581 (p) REVERT: a 74 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8695 (pttp) REVERT: a 92 ARG cc_start: 0.6554 (mmp-170) cc_final: 0.6349 (mmp-170) REVERT: a 188 TRP cc_start: 0.7909 (t60) cc_final: 0.7479 (t-100) REVERT: a 298 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7972 (mmt90) REVERT: a 398 THR cc_start: 0.8674 (t) cc_final: 0.8445 (m) REVERT: a 406 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: a 453 MET cc_start: 0.8327 (mtp) cc_final: 0.8075 (mtp) REVERT: a 752 LEU cc_start: 0.7910 (mt) cc_final: 0.7639 (mt) REVERT: a 759 MET cc_start: 0.6632 (ptt) cc_final: 0.5573 (tmm) outliers start: 139 outliers final: 91 residues processed: 619 average time/residue: 0.3247 time to fit residues: 320.5881 Evaluate side-chains 580 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 480 time to evaluate : 2.618 ------------------------------------------------------------------------------- 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 356 THR 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 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 99 VAL 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 143 LEU 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 140 VAL 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 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 76 ASN 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 367 THR 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: 9.9990 chunk 85 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 298 optimal weight: 20.0000 chunk 246 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24030 Z= 0.319 Angle : 0.729 9.800 32572 Z= 0.375 Chirality : 0.045 0.494 3837 Planarity : 0.005 0.074 4040 Dihedral : 8.403 109.461 3546 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 8.31 % Allowed : 19.25 % Favored : 72.45 % 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: 0.29 (0.15), residues: 3030 helix: 1.07 (0.11), residues: 2125 sheet: -0.77 (0.54), residues: 78 loop : -2.03 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 757 HIS 0.010 0.001 HIS a 766 PHE 0.026 0.002 PHE a 67 TYR 0.022 0.002 TYR b 71 ARG 0.010 0.001 ARG n 119 *********************** 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 720 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 515 time to evaluate : 2.471 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: c 449 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: d 191 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.6457 (t80) REVERT: d 324 LYS cc_start: 0.7692 (ttmm) cc_final: 0.7093 (tttp) REVERT: f 25 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6819 (ttt) REVERT: f 63 GLU cc_start: 0.8013 (pp20) cc_final: 0.7802 (pp20) REVERT: g 10 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5379 (m-80) REVERT: h 23 MET cc_start: 0.5434 (tpt) cc_final: 0.5039 (tpt) REVERT: h 44 MET cc_start: 0.5498 (ptp) cc_final: 0.5153 (ptp) REVERT: h 110 ILE cc_start: 0.6470 (mt) cc_final: 0.6005 (pt) REVERT: h 128 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6239 (t80) REVERT: h 136 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7848 (tt) REVERT: i 36 LYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5514 (tppp) REVERT: i 54 LYS cc_start: 0.7042 (mmtt) cc_final: 0.6453 (mmmt) REVERT: j 108 PHE cc_start: 0.4781 (OUTLIER) cc_final: 0.4380 (m-80) REVERT: k 108 PHE cc_start: 0.6403 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: l 47 MET cc_start: 0.7269 (pmm) cc_final: 0.6381 (pmm) REVERT: n 17 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6948 (ttp) REVERT: o 47 MET cc_start: 0.8343 (tmm) cc_final: 0.7839 (tmm) REVERT: a 11 THR cc_start: 0.4948 (OUTLIER) cc_final: 0.4667 (p) REVERT: a 74 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8633 (pttm) REVERT: a 188 TRP cc_start: 0.8204 (t60) cc_final: 0.7822 (t-100) REVERT: a 398 THR cc_start: 0.8630 (t) cc_final: 0.8339 (m) REVERT: a 403 PHE cc_start: 0.8463 (t80) cc_final: 0.8139 (t80) REVERT: a 406 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8035 (mtp) REVERT: a 453 MET cc_start: 0.8321 (mtp) cc_final: 0.8082 (mtp) REVERT: a 475 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6287 (p90) REVERT: a 752 LEU cc_start: 0.7950 (mt) cc_final: 0.7667 (mt) REVERT: a 759 MET cc_start: 0.6789 (ptt) cc_final: 0.5422 (tmm) outliers start: 205 outliers final: 138 residues processed: 648 average time/residue: 0.3217 time to fit residues: 334.0571 Evaluate side-chains 624 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 473 time to evaluate : 2.614 ------------------------------------------------------------------------------- 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 356 THR 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 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 43 THR 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 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 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 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 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 56 ILE 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 53 MET 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 28 MET Chi-restraints excluded: chain i residue 36 LYS 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 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 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 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 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 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 115 ASP Chi-restraints excluded: chain m residue 121 THR 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 67 ILE Chi-restraints excluded: chain n residue 72 VAL 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 148 VAL 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 e residue 73 ILE Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 71 GLU 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 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 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 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 643 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: 5.9990 chunk 207 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 342 HIS f 36 HIS ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24030 Z= 0.222 Angle : 0.669 9.664 32572 Z= 0.341 Chirality : 0.043 0.465 3837 Planarity : 0.005 0.080 4040 Dihedral : 8.166 110.560 3545 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 7.01 % Allowed : 21.60 % Favored : 71.39 % 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: 0.62 (0.15), residues: 3030 helix: 1.34 (0.11), residues: 2130 sheet: -0.59 (0.61), residues: 62 loop : -1.98 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP a 757 HIS 0.006 0.001 HIS a 766 PHE 0.023 0.002 PHE b 174 TYR 0.020 0.001 TYR a 562 ARG 0.010 0.001 ARG n 119 *********************** 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 686 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 513 time to evaluate : 2.513 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: c 447 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.6545 (p0) REVERT: c 449 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.6603 (m-80) REVERT: b 92 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5584 (mp) REVERT: d 83 GLU cc_start: 0.5518 (mt-10) cc_final: 0.5229 (mt-10) REVERT: d 191 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.6443 (t80) REVERT: d 324 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7059 (tttp) REVERT: d 325 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7586 (mm-30) REVERT: f 25 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6742 (ttt) REVERT: f 63 GLU cc_start: 0.8018 (pp20) cc_final: 0.7772 (pp20) REVERT: g 123 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.5733 (mp10) REVERT: h 23 MET cc_start: 0.5195 (tpt) cc_final: 0.4889 (tpt) REVERT: h 44 MET cc_start: 0.5241 (ptp) cc_final: 0.5012 (ptp) REVERT: h 110 ILE cc_start: 0.6328 (mt) cc_final: 0.5908 (pt) REVERT: h 128 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.5927 (t80) REVERT: h 136 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7817 (tt) REVERT: i 47 MET cc_start: 0.5370 (mtp) cc_final: 0.5002 (mtp) REVERT: i 54 LYS cc_start: 0.6949 (mmtt) cc_final: 0.6498 (mmmt) REVERT: j 108 PHE cc_start: 0.4943 (OUTLIER) cc_final: 0.4561 (m-80) REVERT: k 44 MET cc_start: 0.8011 (tmm) cc_final: 0.7011 (ppp) REVERT: k 108 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.6219 (m-80) REVERT: k 144 TYR cc_start: 0.5855 (m-10) cc_final: 0.5509 (m-10) REVERT: l 17 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5593 (ptt) REVERT: l 47 MET cc_start: 0.7102 (pmm) cc_final: 0.6788 (pmm) REVERT: n 17 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.6951 (ttp) REVERT: o 47 MET cc_start: 0.8328 (tmm) cc_final: 0.7800 (tmm) REVERT: e 59 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: e 63 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7400 (mm) REVERT: a 59 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8689 (mm-30) REVERT: a 74 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8605 (pttp) REVERT: a 398 THR cc_start: 0.8675 (t) cc_final: 0.8388 (m) REVERT: a 403 PHE cc_start: 0.8482 (t80) cc_final: 0.8166 (t80) REVERT: a 406 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7991 (mtp) REVERT: a 580 MET cc_start: 0.7648 (tpp) cc_final: 0.7049 (tpp) REVERT: a 752 LEU cc_start: 0.7984 (mt) cc_final: 0.7693 (mt) REVERT: a 759 MET cc_start: 0.6596 (ptt) cc_final: 0.5688 (tmm) outliers start: 173 outliers final: 108 residues processed: 625 average time/residue: 0.3446 time to fit residues: 344.9087 Evaluate side-chains 592 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 469 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 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 434 THR Chi-restraints excluded: chain c residue 447 ASP Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 27 TYR 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 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 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 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 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 26 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 123 GLN 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 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 28 MET Chi-restraints excluded: chain i residue 52 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 139 GLU 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 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 60 VAL 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 148 VAL 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 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 151 ILE 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 112 ILE Chi-restraints excluded: chain m residue 115 ASP 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 17 MET Chi-restraints excluded: chain n residue 67 ILE 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 112 ILE Chi-restraints excluded: chain o residue 127 LEU 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 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 102 GLU Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 388 GLU 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 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 658 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 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: 8.9990 chunk 4 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 263 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** c 376 ASN c 392 ASN ** d 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 ASN a 473 ASN a 548 HIS a 749 HIS a 766 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 24030 Z= 0.535 Angle : 0.943 13.699 32572 Z= 0.487 Chirality : 0.053 0.555 3837 Planarity : 0.006 0.078 4040 Dihedral : 8.713 105.747 3541 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 10.82 % Allowed : 20.58 % Favored : 68.60 % 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: -0.77 (0.15), residues: 3030 helix: 0.24 (0.11), residues: 2132 sheet: -0.54 (0.74), residues: 45 loop : -2.34 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP a 293 HIS 0.009 0.002 HIS c 391 PHE 0.035 0.003 PHE a 536 TYR 0.031 0.003 TYR c 361 ARG 0.012 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 735 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 468 time to evaluate : 2.370 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 366 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7812 (tm-30) REVERT: c 437 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8848 (tp) REVERT: c 449 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: b 48 PHE cc_start: 0.4552 (m-10) cc_final: 0.4000 (m-80) REVERT: d 34 ASP cc_start: 0.7979 (m-30) cc_final: 0.7302 (m-30) REVERT: d 101 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.6012 (t80) REVERT: d 191 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.6665 (t80) REVERT: f 25 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7088 (ttt) REVERT: f 63 GLU cc_start: 0.8162 (pp20) cc_final: 0.7929 (pp20) REVERT: g 10 TYR cc_start: 0.6704 (OUTLIER) cc_final: 0.5730 (m-80) REVERT: g 112 ILE cc_start: 0.5720 (OUTLIER) cc_final: 0.5495 (mp) REVERT: h 110 ILE cc_start: 0.6221 (mt) cc_final: 0.5786 (pt) REVERT: h 128 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6824 (p90) REVERT: h 136 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8012 (tt) REVERT: h 152 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8065 (mm) REVERT: i 54 LYS cc_start: 0.7217 (mmtt) cc_final: 0.6696 (mmmt) REVERT: i 87 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.5259 (t80) REVERT: j 9 GLU cc_start: 0.6364 (mm-30) cc_final: 0.6023 (mm-30) REVERT: j 108 PHE cc_start: 0.4914 (OUTLIER) cc_final: 0.4406 (m-80) REVERT: k 108 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: l 47 MET cc_start: 0.7153 (pmm) cc_final: 0.6681 (pmm) REVERT: m 61 MET cc_start: 0.7009 (mmt) cc_final: 0.6506 (mmt) REVERT: n 17 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6979 (ttp) REVERT: n 151 ILE cc_start: 0.5378 (OUTLIER) cc_final: 0.5138 (tt) REVERT: o 47 MET cc_start: 0.8311 (tmm) cc_final: 0.7733 (tmm) REVERT: e 63 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7445 (mm) REVERT: a 59 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8598 (mm-30) REVERT: a 62 ASP cc_start: 0.8538 (m-30) cc_final: 0.8097 (m-30) REVERT: a 69 GLU cc_start: 0.8289 (pp20) cc_final: 0.7990 (tm-30) REVERT: a 71 GLU cc_start: 0.8134 (mp0) cc_final: 0.7717 (mp0) REVERT: a 74 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8697 (pttp) REVERT: a 101 PHE cc_start: 0.6523 (m-10) cc_final: 0.6229 (m-10) REVERT: a 277 ASP cc_start: 0.8183 (m-30) cc_final: 0.7555 (t0) REVERT: a 298 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7841 (tmt170) REVERT: a 406 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8214 (mtm) REVERT: a 453 MET cc_start: 0.8200 (mtp) cc_final: 0.7977 (mtp) REVERT: a 475 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6812 (p90) REVERT: a 571 PHE cc_start: 0.7372 (m-80) cc_final: 0.7124 (m-80) REVERT: a 752 LEU cc_start: 0.7901 (mt) cc_final: 0.7595 (mt) REVERT: a 759 MET cc_start: 0.6745 (ptt) cc_final: 0.5496 (tmm) outliers start: 267 outliers final: 195 residues processed: 656 average time/residue: 0.3114 time to fit residues: 331.0612 Evaluate side-chains 655 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 442 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 272 TYR 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 356 THR 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 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 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 70 ILE 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 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 81 VAL Chi-restraints excluded: chain d residue 101 PHE 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 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 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 64 ILE Chi-restraints excluded: chain h residue 71 VAL 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 113 VAL Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 129 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 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 72 VAL Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 97 LEU 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 60 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 89 SER 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 147 ILE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain l residue 37 SER 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 113 VAL Chi-restraints excluded: chain l residue 136 ILE 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 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 115 ASP Chi-restraints excluded: chain m residue 121 THR 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 m residue 153 SER 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 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 151 ILE Chi-restraints excluded: chain o residue 7 ASN Chi-restraints excluded: chain o residue 16 VAL Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 112 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 619 VAL 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 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 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 576 GLU 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 806 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 294 optimal weight: 6.9990 chunk 244 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 364 HIS c 376 ASN c 392 ASN ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN a 524 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24030 Z= 0.215 Angle : 0.699 9.411 32572 Z= 0.354 Chirality : 0.043 0.481 3837 Planarity : 0.005 0.062 4040 Dihedral : 8.101 103.665 3541 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 5.75 % Allowed : 26.26 % Favored : 67.99 % 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: 0.30 (0.15), residues: 3030 helix: 1.12 (0.11), residues: 2129 sheet: -0.80 (0.65), residues: 57 loop : -2.12 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP a 293 HIS 0.010 0.001 HIS d 313 PHE 0.028 0.002 PHE b 174 TYR 0.023 0.002 TYR d 153 ARG 0.012 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 632 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 490 time to evaluate : 2.762 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: c 447 ASP cc_start: 0.7550 (t70) cc_final: 0.6666 (p0) REVERT: c 449 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: b 68 TRP cc_start: 0.8554 (OUTLIER) cc_final: 0.7980 (t60) REVERT: d 34 ASP cc_start: 0.7849 (m-30) cc_final: 0.7180 (m-30) REVERT: d 191 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.6547 (t80) REVERT: f 25 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6763 (ttt) REVERT: f 63 GLU cc_start: 0.8068 (pp20) cc_final: 0.7828 (pp20) REVERT: g 10 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.5365 (m-80) REVERT: g 112 ILE cc_start: 0.5620 (OUTLIER) cc_final: 0.5368 (mp) REVERT: g 119 ARG cc_start: 0.5913 (ttm170) cc_final: 0.5656 (tpp80) REVERT: h 41 ILE cc_start: 0.6000 (pt) cc_final: 0.5680 (tt) REVERT: h 110 ILE cc_start: 0.6392 (mt) cc_final: 0.5968 (pt) REVERT: h 136 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7818 (tt) REVERT: h 144 TYR cc_start: 0.6594 (m-10) cc_final: 0.5945 (m-10) REVERT: i 54 LYS cc_start: 0.7032 (mmtt) cc_final: 0.6550 (mmmt) REVERT: j 108 PHE cc_start: 0.5101 (OUTLIER) cc_final: 0.4670 (m-80) REVERT: k 44 MET cc_start: 0.8163 (tmm) cc_final: 0.6952 (ppp) REVERT: k 108 PHE cc_start: 0.6319 (OUTLIER) cc_final: 0.6096 (m-80) REVERT: l 47 MET cc_start: 0.6939 (pmm) cc_final: 0.6662 (pmm) REVERT: m 61 MET cc_start: 0.6841 (mmt) cc_final: 0.6355 (mmt) REVERT: n 17 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7324 (tmm) REVERT: n 23 MET cc_start: 0.7944 (tpp) cc_final: 0.7689 (tpt) REVERT: o 47 MET cc_start: 0.8326 (tmm) cc_final: 0.7838 (tmm) REVERT: a 59 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8543 (mm-30) REVERT: a 62 ASP cc_start: 0.8461 (m-30) cc_final: 0.8026 (m-30) REVERT: a 69 GLU cc_start: 0.8357 (pp20) cc_final: 0.8136 (tm-30) REVERT: a 71 GLU cc_start: 0.8232 (mp0) cc_final: 0.7893 (mp0) REVERT: a 74 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8623 (pttp) REVERT: a 257 MET cc_start: 0.7810 (ptp) cc_final: 0.7475 (ptp) REVERT: a 277 ASP cc_start: 0.8121 (m-30) cc_final: 0.7605 (t0) REVERT: a 398 THR cc_start: 0.8704 (t) cc_final: 0.8375 (m) REVERT: a 406 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7999 (mtp) REVERT: a 453 MET cc_start: 0.8178 (mtp) cc_final: 0.7863 (mtp) REVERT: a 475 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.6120 (p90) REVERT: a 580 MET cc_start: 0.8044 (tpp) cc_final: 0.7640 (tpp) REVERT: a 752 LEU cc_start: 0.7794 (mt) cc_final: 0.7518 (mt) REVERT: a 759 MET cc_start: 0.6700 (ptt) cc_final: 0.5452 (tmm) outliers start: 142 outliers final: 97 residues processed: 586 average time/residue: 0.3543 time to fit residues: 334.5860 Evaluate side-chains 564 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 455 time to evaluate : 2.514 ------------------------------------------------------------------------------- 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 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 449 PHE Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 31 ASP 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 196 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 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 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 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 112 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 53 MET Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 74 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 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 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 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 59 VAL 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 150 LEU Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 143 LEU 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 97 LEU Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 112 ILE 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 56 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER 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 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 658 ILE Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 779 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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** c 376 ASN c 392 ASN ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 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** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 ASN j 124 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 637 GLN a 749 HIS a 766 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 24030 Z= 0.366 Angle : 0.799 10.349 32572 Z= 0.408 Chirality : 0.047 0.511 3837 Planarity : 0.005 0.073 4040 Dihedral : 8.253 105.750 3540 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 7.78 % Allowed : 25.36 % Favored : 66.86 % 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: -0.12 (0.15), residues: 3030 helix: 0.78 (0.11), residues: 2135 sheet: -0.65 (0.68), residues: 55 loop : -2.24 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 293 HIS 0.015 0.001 HIS d 313 PHE 0.041 0.002 PHE b 48 TYR 0.028 0.002 TYR c 361 ARG 0.014 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 655 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 463 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 449 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: d 34 ASP cc_start: 0.7939 (m-30) cc_final: 0.7201 (m-30) REVERT: d 101 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.5843 (t80) REVERT: d 191 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.6595 (t80) REVERT: f 25 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6842 (ttt) REVERT: f 63 GLU cc_start: 0.8228 (pp20) cc_final: 0.7927 (pp20) REVERT: g 10 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: g 112 ILE cc_start: 0.5698 (OUTLIER) cc_final: 0.5470 (mp) REVERT: g 123 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.5710 (mp10) REVERT: h 110 ILE cc_start: 0.6251 (mt) cc_final: 0.5799 (pt) REVERT: i 54 LYS cc_start: 0.7184 (mmtt) cc_final: 0.6708 (mmmt) REVERT: i 139 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6464 (tm-30) REVERT: j 108 PHE cc_start: 0.5094 (OUTLIER) cc_final: 0.4769 (m-80) REVERT: k 108 PHE cc_start: 0.6358 (OUTLIER) cc_final: 0.6089 (m-80) REVERT: l 47 MET cc_start: 0.7241 (pmm) cc_final: 0.6939 (pmm) REVERT: m 61 MET cc_start: 0.7050 (mmt) cc_final: 0.6598 (mmt) REVERT: n 17 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.6928 (ttp) REVERT: n 151 ILE cc_start: 0.5023 (OUTLIER) cc_final: 0.4809 (tt) REVERT: o 47 MET cc_start: 0.8337 (tmm) cc_final: 0.7837 (tmm) REVERT: o 131 MET cc_start: 0.6292 (tmm) cc_final: 0.5808 (tmm) REVERT: e 63 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7470 (mm) REVERT: a 59 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8578 (mm-30) REVERT: a 62 ASP cc_start: 0.8599 (m-30) cc_final: 0.8054 (m-30) REVERT: a 69 GLU cc_start: 0.8317 (pp20) cc_final: 0.8049 (tm-30) REVERT: a 71 GLU cc_start: 0.8461 (mp0) cc_final: 0.8092 (mp0) REVERT: a 74 LYS cc_start: 0.9032 (mmmt) cc_final: 0.8678 (pttp) REVERT: a 277 ASP cc_start: 0.8129 (m-30) cc_final: 0.7541 (t0) REVERT: a 298 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7849 (tmt170) REVERT: a 398 THR cc_start: 0.8778 (t) cc_final: 0.8447 (m) REVERT: a 406 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8092 (mtp) REVERT: a 475 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6510 (p90) REVERT: a 580 MET cc_start: 0.8154 (tpp) cc_final: 0.7612 (tpp) REVERT: a 752 LEU cc_start: 0.7846 (mt) cc_final: 0.7556 (mt) REVERT: a 759 MET cc_start: 0.6724 (ptt) cc_final: 0.5581 (tmm) outliers start: 192 outliers final: 141 residues processed: 594 average time/residue: 0.3163 time to fit residues: 301.9973 Evaluate side-chains 607 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 451 time to evaluate : 2.547 ------------------------------------------------------------------------------- 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 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 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL 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 31 ASP 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 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 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 205 THR Chi-restraints excluded: chain d residue 214 LEU 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 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 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 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 132 ILE 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 56 ILE Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 147 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 136 ILE Chi-restraints excluded: chain i residue 139 GLU 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 52 ILE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 72 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 124 GLN 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 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 147 ILE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain k residue 151 ILE 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 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 151 ILE Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 52 ILE 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 151 ILE Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 112 ILE 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 56 ILE Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 76 ASN Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 188 TRP Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 367 THR 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 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 725 THR 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 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: 6.9990 chunk 174 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 186 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 349 HIS c 376 ASN c 392 ASN ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 313 HIS d 330 ASN ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 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 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 24030 Z= 0.217 Angle : 0.708 10.225 32572 Z= 0.355 Chirality : 0.043 0.460 3837 Planarity : 0.005 0.064 4040 Dihedral : 7.802 102.633 3538 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 4.74 % Allowed : 28.85 % Favored : 66.41 % 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: 1.22 (0.11), residues: 2141 sheet: -0.92 (0.60), residues: 66 loop : -2.24 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 757 HIS 0.007 0.001 HIS d 313 PHE 0.031 0.002 PHE b 174 TYR 0.024 0.002 TYR d 153 ARG 0.013 0.001 ARG n 119 *********************** 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 595 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 478 time to evaluate : 2.409 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: c 447 ASP cc_start: 0.7572 (t70) cc_final: 0.6649 (p0) REVERT: c 449 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: b 68 TRP cc_start: 0.8542 (OUTLIER) cc_final: 0.8053 (t60) REVERT: d 107 MET cc_start: 0.6577 (mtp) cc_final: 0.5461 (mtp) REVERT: d 149 PRO cc_start: 0.6705 (Cg_exo) cc_final: 0.6501 (Cg_endo) REVERT: d 191 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6574 (t80) REVERT: d 326 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7928 (mm-40) REVERT: f 63 GLU cc_start: 0.8034 (pp20) cc_final: 0.7772 (pp20) REVERT: g 119 ARG cc_start: 0.5949 (ttm170) cc_final: 0.5449 (tpp80) REVERT: g 123 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.5597 (mp10) REVERT: h 41 ILE cc_start: 0.5796 (pt) cc_final: 0.5478 (tt) REVERT: h 44 MET cc_start: 0.5370 (ptp) cc_final: 0.5102 (ptp) REVERT: h 110 ILE cc_start: 0.6376 (mt) cc_final: 0.5925 (pt) REVERT: i 23 MET cc_start: 0.4085 (ptm) cc_final: 0.3859 (ptm) REVERT: i 54 LYS cc_start: 0.7039 (mmtt) cc_final: 0.6621 (mmmt) REVERT: j 17 MET cc_start: 0.7327 (ttt) cc_final: 0.7055 (ttm) REVERT: j 108 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.4934 (m-80) REVERT: k 44 MET cc_start: 0.8239 (tmm) cc_final: 0.6870 (ppp) REVERT: k 108 PHE cc_start: 0.6299 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: m 61 MET cc_start: 0.6874 (mmt) cc_final: 0.6458 (mmt) REVERT: n 23 MET cc_start: 0.8027 (tpp) cc_final: 0.7803 (tpt) REVERT: o 47 MET cc_start: 0.8327 (tmm) cc_final: 0.7810 (tmm) REVERT: o 126 ARG cc_start: 0.8169 (mtp180) cc_final: 0.7709 (ttm170) REVERT: o 131 MET cc_start: 0.6194 (tmm) cc_final: 0.5664 (tmm) REVERT: p 636 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7407 (pt) REVERT: a 62 ASP cc_start: 0.8507 (m-30) cc_final: 0.8013 (m-30) REVERT: a 69 GLU cc_start: 0.8344 (pp20) cc_final: 0.8118 (tm-30) REVERT: a 71 GLU cc_start: 0.8348 (mp0) cc_final: 0.7983 (mp0) REVERT: a 74 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8711 (pttp) REVERT: a 188 TRP cc_start: 0.7250 (OUTLIER) cc_final: 0.7032 (t-100) REVERT: a 189 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8273 (mtt180) REVERT: a 277 ASP cc_start: 0.8071 (m-30) cc_final: 0.7482 (t0) REVERT: a 398 THR cc_start: 0.8675 (t) cc_final: 0.8331 (m) REVERT: a 406 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7988 (mtp) REVERT: a 475 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5923 (p90) REVERT: a 580 MET cc_start: 0.8057 (tpp) cc_final: 0.7654 (tpp) REVERT: a 665 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7519 (mmm160) REVERT: a 752 LEU cc_start: 0.7785 (mt) cc_final: 0.7500 (mt) REVERT: a 759 MET cc_start: 0.6670 (ptt) cc_final: 0.5536 (tmm) outliers start: 117 outliers final: 89 residues processed: 551 average time/residue: 0.3223 time to fit residues: 281.7097 Evaluate side-chains 556 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 457 time to evaluate : 2.476 ------------------------------------------------------------------------------- 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 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 437 LEU Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 43 THR 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 196 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 308 PHE 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 26 SER Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 123 GLN 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 108 PHE Chi-restraints excluded: chain i residue 28 MET 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 146 LEU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 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 17 MET Chi-restraints excluded: chain k residue 53 MET 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 150 LEU Chi-restraints excluded: chain l residue 75 LEU 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 115 ASP 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 52 ILE 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 148 VAL Chi-restraints excluded: chain o residue 150 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 44 THR Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 188 TRP Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 475 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 658 ILE Chi-restraints excluded: chain a residue 763 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 5.9990 chunk 280 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 273 optimal weight: 0.2980 chunk 164 optimal weight: 6.9990 chunk 118 optimal weight: 0.0770 chunk 214 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 246 optimal weight: 20.0000 chunk 258 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN n 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3625 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= 0.249 Angle : 0.718 15.264 32572 Z= 0.359 Chirality : 0.043 0.450 3837 Planarity : 0.005 0.069 4040 Dihedral : 7.742 103.123 3538 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 4.70 % Allowed : 28.89 % Favored : 66.41 % 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: 0.41 (0.15), residues: 3030 helix: 1.23 (0.11), residues: 2133 sheet: -0.66 (0.66), residues: 57 loop : -2.20 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP a 757 HIS 0.015 0.001 HIS d 313 PHE 0.027 0.002 PHE b 174 TYR 0.021 0.002 TYR d 153 ARG 0.014 0.001 ARG n 119 *********************** 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 574 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 458 time to evaluate : 2.448 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: c 447 ASP cc_start: 0.7627 (t70) cc_final: 0.6697 (p0) REVERT: c 449 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6681 (m-80) REVERT: d 34 ASP cc_start: 0.7915 (m-30) cc_final: 0.7228 (m-30) REVERT: d 107 MET cc_start: 0.6418 (mtp) cc_final: 0.5413 (mtp) REVERT: d 149 PRO cc_start: 0.6908 (Cg_exo) cc_final: 0.6703 (Cg_endo) REVERT: d 191 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6574 (t80) REVERT: f 63 GLU cc_start: 0.8050 (pp20) cc_final: 0.7807 (pp20) REVERT: g 112 ILE cc_start: 0.5362 (OUTLIER) cc_final: 0.5119 (mp) REVERT: g 119 ARG cc_start: 0.5924 (ttm170) cc_final: 0.5484 (tpp80) REVERT: g 123 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.5559 (mp10) REVERT: h 41 ILE cc_start: 0.5865 (pt) cc_final: 0.5604 (tt) REVERT: h 44 MET cc_start: 0.5218 (ptp) cc_final: 0.4992 (ptp) REVERT: h 110 ILE cc_start: 0.6295 (mt) cc_final: 0.5874 (pt) REVERT: i 54 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6639 (mmmt) REVERT: i 139 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6387 (tm-30) REVERT: j 17 MET cc_start: 0.7364 (ttt) cc_final: 0.7091 (ttm) REVERT: j 108 PHE cc_start: 0.5159 (OUTLIER) cc_final: 0.4788 (m-80) REVERT: k 44 MET cc_start: 0.8136 (tmm) cc_final: 0.6848 (ppp) REVERT: k 108 PHE cc_start: 0.6289 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: m 48 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8142 (mtm110) REVERT: m 61 MET cc_start: 0.6980 (mmt) cc_final: 0.6554 (mmt) REVERT: o 47 MET cc_start: 0.8321 (tmm) cc_final: 0.7794 (tmm) REVERT: o 126 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7741 (ttm170) REVERT: o 131 MET cc_start: 0.6191 (tmm) cc_final: 0.5606 (tmm) REVERT: a 59 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8402 (pt0) REVERT: a 62 ASP cc_start: 0.8489 (m-30) cc_final: 0.8243 (m-30) REVERT: a 69 GLU cc_start: 0.8294 (pp20) cc_final: 0.8054 (tm-30) REVERT: a 71 GLU cc_start: 0.8439 (mp0) cc_final: 0.7955 (mp0) REVERT: a 74 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8727 (pttp) REVERT: a 188 TRP cc_start: 0.7351 (OUTLIER) cc_final: 0.7080 (t-100) REVERT: a 277 ASP cc_start: 0.8119 (m-30) cc_final: 0.7535 (t0) REVERT: a 398 THR cc_start: 0.8696 (t) cc_final: 0.8369 (m) REVERT: a 406 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7965 (mtp) REVERT: a 580 MET cc_start: 0.8114 (tpp) cc_final: 0.7683 (tpp) REVERT: a 665 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7588 (mmm160) REVERT: a 752 LEU cc_start: 0.7770 (mt) cc_final: 0.7479 (mt) REVERT: a 759 MET cc_start: 0.6701 (ptt) cc_final: 0.5613 (tmm) outliers start: 116 outliers final: 100 residues processed: 538 average time/residue: 0.3228 time to fit residues: 278.3436 Evaluate side-chains 559 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 450 time to evaluate : 2.738 ------------------------------------------------------------------------------- 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 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 449 PHE Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 43 THR 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 196 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 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 75 LEU Chi-restraints excluded: chain f residue 79 LEU 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 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 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 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 146 LEU Chi-restraints excluded: chain i residue 153 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 124 GLN Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 17 MET 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 150 LEU 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 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 52 ILE 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 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 615 LEU Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 188 TRP Chi-restraints excluded: chain a residue 195 VAL 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 390 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 471 SER 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 657 LEU Chi-restraints excluded: chain a residue 658 ILE 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: 1.9990 chunk 288 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 129 HIS ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 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 749 HIS a 766 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24030 Z= 0.257 Angle : 0.741 16.241 32572 Z= 0.369 Chirality : 0.044 0.452 3837 Planarity : 0.005 0.069 4040 Dihedral : 7.713 101.859 3538 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 4.78 % Allowed : 28.97 % Favored : 66.25 % 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: 0.36 (0.15), residues: 3030 helix: 1.18 (0.11), residues: 2145 sheet: -0.69 (0.67), residues: 57 loop : -2.21 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP a 757 HIS 0.015 0.001 HIS d 313 PHE 0.028 0.002 PHE b 174 TYR 0.052 0.002 TYR l 144 ARG 0.015 0.001 ARG n 119 ********************** 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 576 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 458 time to evaluate : 2.521 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: c 447 ASP cc_start: 0.7636 (t70) cc_final: 0.6666 (p0) REVERT: c 449 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: d 34 ASP cc_start: 0.7931 (m-30) cc_final: 0.7235 (m-30) REVERT: d 107 MET cc_start: 0.6540 (mtp) cc_final: 0.5556 (mtp) REVERT: d 149 PRO cc_start: 0.6751 (Cg_exo) cc_final: 0.6545 (Cg_endo) REVERT: d 191 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6580 (t80) REVERT: f 63 GLU cc_start: 0.8124 (pp20) cc_final: 0.7862 (pp20) REVERT: g 112 ILE cc_start: 0.5519 (OUTLIER) cc_final: 0.5251 (mp) REVERT: g 119 ARG cc_start: 0.5920 (ttm170) cc_final: 0.5461 (tpp80) REVERT: g 123 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.5579 (mp10) REVERT: h 41 ILE cc_start: 0.5861 (pt) cc_final: 0.5615 (tt) REVERT: h 110 ILE cc_start: 0.6298 (mt) cc_final: 0.5877 (pt) REVERT: i 54 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6640 (mmmt) REVERT: i 139 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6382 (tm-30) REVERT: j 17 MET cc_start: 0.7324 (ttt) cc_final: 0.7057 (ttm) REVERT: j 108 PHE cc_start: 0.5161 (OUTLIER) cc_final: 0.4795 (m-80) REVERT: k 44 MET cc_start: 0.8135 (tmm) cc_final: 0.6865 (ppp) REVERT: k 108 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: m 61 MET cc_start: 0.6938 (mmt) cc_final: 0.6532 (mmt) REVERT: n 23 MET cc_start: 0.8353 (tpp) cc_final: 0.8119 (tpt) REVERT: o 47 MET cc_start: 0.8323 (tmm) cc_final: 0.7907 (tmm) REVERT: o 131 MET cc_start: 0.6123 (tmm) cc_final: 0.5517 (tmm) REVERT: a 62 ASP cc_start: 0.8517 (m-30) cc_final: 0.8050 (m-30) REVERT: a 69 GLU cc_start: 0.8287 (pp20) cc_final: 0.8060 (tm-30) REVERT: a 71 GLU cc_start: 0.8419 (mp0) cc_final: 0.8045 (mp0) REVERT: a 74 LYS cc_start: 0.9085 (mmmt) cc_final: 0.8716 (pttp) REVERT: a 277 ASP cc_start: 0.8036 (m-30) cc_final: 0.7529 (t0) REVERT: a 284 GLN cc_start: 0.8132 (mt0) cc_final: 0.7855 (mt0) REVERT: a 398 THR cc_start: 0.8707 (t) cc_final: 0.8375 (m) REVERT: a 406 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: a 482 ARG cc_start: 0.6805 (tpt-90) cc_final: 0.6437 (tpt-90) REVERT: a 580 MET cc_start: 0.8097 (tpp) cc_final: 0.7680 (tpp) REVERT: a 752 LEU cc_start: 0.7764 (mt) cc_final: 0.7474 (mt) REVERT: a 759 MET cc_start: 0.6674 (ptt) cc_final: 0.5638 (tmm) outliers start: 118 outliers final: 101 residues processed: 542 average time/residue: 0.3171 time to fit residues: 276.2699 Evaluate side-chains 560 residues out of total 2468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 451 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 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 449 PHE Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 43 THR 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 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 196 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 275 GLU 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 75 LEU Chi-restraints excluded: chain f residue 79 LEU 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 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 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 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 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 17 MET 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 150 LEU 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 112 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 52 ILE 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 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 615 LEU Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 188 TRP Chi-restraints excluded: chain a residue 195 VAL 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 390 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 455 LEU 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 657 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 730 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: 0.6980 chunk 256 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 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 749 HIS a 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.160250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135316 restraints weight = 44701.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.138818 restraints weight = 21140.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140979 restraints weight = 12497.834| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.3784 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= 0.253 Angle : 0.739 14.071 32572 Z= 0.368 Chirality : 0.044 0.451 3837 Planarity : 0.005 0.069 4040 Dihedral : 7.669 100.324 3538 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 5.23 % Allowed : 28.65 % Favored : 66.13 % 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: 2145 sheet: -0.68 (0.67), residues: 57 loop : -2.22 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP a 757 HIS 0.015 0.001 HIS d 313 PHE 0.028 0.002 PHE b 174 TYR 0.042 0.002 TYR l 144 ARG 0.015 0.001 ARG n 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5483.62 seconds wall clock time: 98 minutes 14.06 seconds (5894.06 seconds total)