Starting phenix.real_space_refine on Sat Jan 25 09:37:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bry_44845/01_2025/9bry_44845.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bry_44845/01_2025/9bry_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/cci-nas-00/data/ceres_data/9bry_44845/01_2025/9bry_44845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bry_44845/01_2025/9bry_44845.map" model { file = "/net/cci-nas-00/data/ceres_data/9bry_44845/01_2025/9bry_44845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bry_44845/01_2025/9bry_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. Time to flip 36 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23530 Number of models: 1 Model: "" Number of chains: 20 Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "f" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 666 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "e" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "a" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6039 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 31, 'TRANS': 711} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.06, per 1000 atoms: 0.51 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 - 3.00 Amino acid : True - 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: 5.91 Conformation dependent library (CDL) restraints added in 3.4 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: 2.01 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: 7.28 Time building geometry restraints manager: 6.76 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: 0.00 - 2.68: 31878 2.68 - 5.36: 600 5.36 - 8.04: 83 8.04 - 10.73: 8 10.73 - 13.41: 3 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: 1.060 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: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 46.610 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.280 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 71 poor density : 582 time to evaluate : 2.625 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: 0.3619 time to fit residues: 356.8356 Evaluate side-chains 557 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 499 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.161727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.136237 restraints weight = 43731.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.139868 restraints weight = 21003.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.142183 restraints weight = 12425.515| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 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 to be fit. rotamer outliers: 139 poor density : 534 time to evaluate : 2.542 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: 0.7437 (t70) cc_final: 0.6525 (p0) REVERT: c 448 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7447 (ttm110) REVERT: c 449 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: b 174 PHE cc_start: 0.7777 (t80) cc_final: 0.7526 (t80) REVERT: d 83 GLU cc_start: 0.5367 (mt-10) cc_final: 0.5113 (mt-10) REVERT: d 87 MET cc_start: 0.7463 (mmt) cc_final: 0.7227 (tpp) REVERT: d 139 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6289 (pm20) REVERT: d 191 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.6298 (t80) REVERT: d 324 LYS cc_start: 0.7637 (ttmm) cc_final: 0.6986 (tttp) REVERT: g 17 MET cc_start: 0.6362 (ttm) cc_final: 0.5971 (tpt) REVERT: h 41 ILE cc_start: 0.5940 (pt) cc_final: 0.5616 (tt) REVERT: h 110 ILE cc_start: 0.6339 (mt) cc_final: 0.5952 (pt) REVERT: h 128 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6490 (t80) REVERT: h 136 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7598 (tt) REVERT: i 54 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6407 (mmmt) REVERT: j 44 MET cc_start: 0.6031 (tmm) cc_final: 0.5770 (tmm) REVERT: j 108 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.4022 (m-80) REVERT: j 133 LEU cc_start: 0.5154 (tp) cc_final: 0.4915 (tt) REVERT: k 44 MET cc_start: 0.7993 (tmm) cc_final: 0.7328 (ppp) REVERT: k 57 ILE cc_start: 0.8111 (mm) cc_final: 0.7853 (mp) REVERT: k 108 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.6167 (m-80) REVERT: l 23 MET cc_start: 0.6316 (tpt) cc_final: 0.6102 (tpt) REVERT: l 47 MET cc_start: 0.7128 (pmm) cc_final: 0.6296 (pmm) REVERT: m 48 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8483 (mmm-85) REVERT: m 155 LYS cc_start: 0.6712 (tptt) cc_final: 0.6497 (tptp) REVERT: o 47 MET cc_start: 0.8500 (tmm) cc_final: 0.7944 (tmm) REVERT: a 11 THR cc_start: 0.4919 (OUTLIER) cc_final: 0.4560 (p) REVERT: a 74 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8685 (pttp) REVERT: a 92 ARG cc_start: 0.6771 (mmp-170) cc_final: 0.6531 (mmp-170) REVERT: a 179 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6609 (mtm180) REVERT: a 188 TRP cc_start: 0.7847 (t60) cc_final: 0.7360 (t-100) REVERT: a 298 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7990 (mmt90) REVERT: a 395 THR cc_start: 0.8083 (m) cc_final: 0.7854 (p) REVERT: a 406 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8019 (mtp) REVERT: a 453 MET cc_start: 0.8324 (mtp) cc_final: 0.8048 (mtp) REVERT: a 752 LEU cc_start: 0.8050 (mt) cc_final: 0.7749 (mt) REVERT: a 759 MET cc_start: 0.6920 (ptt) cc_final: 0.5640 (tmm) outliers start: 139 outliers final: 91 residues processed: 619 average time/residue: 0.3342 time to fit residues: 329.5135 Evaluate side-chains 583 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 482 time to evaluate : 2.658 ------------------------------------------------------------------------------- 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 179 ARG 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 189 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 392 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 548 HIS ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.155408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129926 restraints weight = 44862.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133302 restraints weight = 21773.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135459 restraints weight = 13075.846| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 24030 Z= 0.429 Angle : 0.832 10.441 32572 Z= 0.430 Chirality : 0.048 0.482 3837 Planarity : 0.006 0.079 4040 Dihedral : 8.749 108.154 3546 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 9.40 % Allowed : 19.89 % Favored : 70.71 % 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: -0.27 (0.15), residues: 3030 helix: 0.64 (0.11), residues: 2123 sheet: -0.23 (0.74), residues: 42 loop : -2.21 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 333 HIS 0.011 0.001 HIS a 766 PHE 0.034 0.003 PHE a 67 TYR 0.026 0.002 TYR b 71 ARG 0.017 0.001 ARG d 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 504 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 449 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: d 34 ASP cc_start: 0.8053 (m-30) cc_final: 0.7324 (m-30) REVERT: d 191 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.6451 (t80) REVERT: d 324 LYS cc_start: 0.7553 (ttmm) cc_final: 0.6939 (tttp) REVERT: d 325 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8013 (mm-30) REVERT: f 25 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6873 (ttt) REVERT: g 10 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: g 47 MET cc_start: 0.7341 (tpp) cc_final: 0.7101 (tpp) REVERT: h 23 MET cc_start: 0.5394 (tpt) cc_final: 0.5053 (tpt) REVERT: h 44 MET cc_start: 0.5315 (ptp) cc_final: 0.5071 (ptp) REVERT: h 110 ILE cc_start: 0.6265 (mt) cc_final: 0.5817 (pt) REVERT: h 128 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6291 (t80) REVERT: h 136 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7842 (tt) REVERT: i 54 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6478 (mmmt) REVERT: j 108 PHE cc_start: 0.4686 (OUTLIER) cc_final: 0.4208 (m-80) REVERT: k 108 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: k 147 ILE cc_start: 0.7618 (mt) cc_final: 0.7409 (mt) REVERT: l 23 MET cc_start: 0.6724 (tpt) cc_final: 0.6441 (tpt) REVERT: l 47 MET cc_start: 0.7415 (pmm) cc_final: 0.6441 (pmm) REVERT: m 48 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8489 (mmm-85) REVERT: n 17 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6893 (ttp) REVERT: o 47 MET cc_start: 0.8481 (tmm) cc_final: 0.7880 (tmm) REVERT: e 63 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7388 (mm) REVERT: a 11 THR cc_start: 0.4824 (OUTLIER) cc_final: 0.4523 (p) REVERT: a 74 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8572 (pttm) REVERT: a 188 TRP cc_start: 0.8180 (t60) cc_final: 0.7848 (t-100) REVERT: a 291 ARG cc_start: 0.6764 (mmp80) cc_final: 0.6322 (mmp80) REVERT: a 395 THR cc_start: 0.8070 (m) cc_final: 0.7830 (p) REVERT: a 406 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7982 (mtp) REVERT: a 475 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6599 (p90) REVERT: a 628 MET cc_start: 0.6290 (mtt) cc_final: 0.5902 (mtm) REVERT: a 752 LEU cc_start: 0.8074 (mt) cc_final: 0.7767 (mt) REVERT: a 759 MET cc_start: 0.7018 (ptt) cc_final: 0.5751 (tmm) REVERT: a 786 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7114 (tp) outliers start: 232 outliers final: 156 residues processed: 660 average time/residue: 0.3375 time to fit residues: 357.8385 Evaluate side-chains 626 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 456 time to evaluate : 2.604 ------------------------------------------------------------------------------- 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 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 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 103 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 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 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 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 60 VAL Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 113 VAL Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain i residue 24 VAL 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 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 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 80 LEU Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 44 MET Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 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 71 VAL 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 16 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 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 11 THR Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 76 ASN 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 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 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 620 SER Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 657 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 726 ILE Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 786 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 187 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 364 HIS 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.161004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.135778 restraints weight = 44117.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139373 restraints weight = 20891.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.141659 restraints weight = 12310.357| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24030 Z= 0.222 Angle : 0.682 9.599 32572 Z= 0.349 Chirality : 0.043 0.478 3837 Planarity : 0.005 0.063 4040 Dihedral : 8.303 109.546 3545 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 6.32 % Allowed : 23.22 % Favored : 70.46 % 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: 0.44 (0.15), residues: 3030 helix: 1.19 (0.11), residues: 2135 sheet: -0.62 (0.61), residues: 62 loop : -2.01 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 757 HIS 0.007 0.001 HIS a 766 PHE 0.021 0.002 PHE a 475 TYR 0.019 0.002 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 672 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 516 time to evaluate : 2.314 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: 0.7637 (OUTLIER) cc_final: 0.6586 (p0) REVERT: c 449 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6530 (m-80) REVERT: d 83 GLU cc_start: 0.5542 (mt-10) cc_final: 0.5142 (mt-10) REVERT: d 101 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.5556 (t80) REVERT: d 191 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.6262 (t80) REVERT: d 324 LYS cc_start: 0.7337 (ttmm) cc_final: 0.6722 (tttp) REVERT: f 25 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6721 (ttt) REVERT: g 47 MET cc_start: 0.7298 (tpp) cc_final: 0.7066 (tpp) REVERT: g 123 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.5694 (mp10) REVERT: h 23 MET cc_start: 0.5254 (tpt) cc_final: 0.4959 (tpt) REVERT: h 110 ILE cc_start: 0.6261 (mt) cc_final: 0.5842 (pt) REVERT: h 128 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.5933 (t80) REVERT: h 136 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7621 (tt) REVERT: h 144 TYR cc_start: 0.6695 (m-10) cc_final: 0.6318 (m-10) REVERT: i 54 LYS cc_start: 0.7092 (mmtt) cc_final: 0.6463 (mmmt) REVERT: j 108 PHE cc_start: 0.4848 (OUTLIER) cc_final: 0.4529 (m-80) REVERT: k 44 MET cc_start: 0.8238 (tmm) cc_final: 0.7076 (ppp) REVERT: k 108 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6215 (m-80) REVERT: l 23 MET cc_start: 0.6562 (tpt) cc_final: 0.6262 (tpt) REVERT: l 47 MET cc_start: 0.7090 (pmm) cc_final: 0.6688 (pmm) REVERT: l 87 TYR cc_start: 0.6603 (t80) cc_final: 0.6297 (t80) REVERT: m 48 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8427 (mmm-85) REVERT: n 17 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.6855 (ttp) REVERT: o 47 MET cc_start: 0.8500 (tmm) cc_final: 0.7866 (tmm) REVERT: e 59 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.7086 (mt0) REVERT: a 59 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8157 (pt0) REVERT: a 74 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8599 (pttp) REVERT: a 101 PHE cc_start: 0.5873 (m-10) cc_final: 0.5529 (m-10) REVERT: a 395 THR cc_start: 0.8014 (m) cc_final: 0.7772 (p) REVERT: a 406 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7965 (mtp) REVERT: a 475 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6405 (p90) REVERT: a 571 PHE cc_start: 0.7159 (m-80) cc_final: 0.6867 (m-80) REVERT: a 580 MET cc_start: 0.7742 (tpp) cc_final: 0.7054 (tpp) REVERT: a 752 LEU cc_start: 0.8091 (mt) cc_final: 0.7774 (mt) REVERT: a 759 MET cc_start: 0.6945 (ptt) cc_final: 0.5749 (tmm) outliers start: 156 outliers final: 107 residues processed: 611 average time/residue: 0.3463 time to fit residues: 336.9820 Evaluate side-chains 588 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 467 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 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 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 b residue 197 LEU Chi-restraints excluded: chain d residue 101 PHE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 26 LEU 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 72 VAL 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 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 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 59 VAL 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 136 ILE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 37 SER 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 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 17 MET Chi-restraints excluded: chain n residue 52 ILE 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 64 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 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 123 LEU 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 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 763 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 182 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 392 ASN ** 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** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 473 ASN a 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.157097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131849 restraints weight = 44940.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135301 restraints weight = 21498.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.137495 restraints weight = 12779.416| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.3003 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= 0.334 Angle : 0.760 10.019 32572 Z= 0.387 Chirality : 0.046 0.489 3837 Planarity : 0.005 0.070 4040 Dihedral : 8.280 107.587 3542 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 8.75 % Allowed : 22.41 % Favored : 68.84 % 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: 0.08 (0.15), residues: 3030 helix: 0.93 (0.11), residues: 2139 sheet: -0.21 (0.76), residues: 42 loop : -2.18 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP a 293 HIS 0.007 0.001 HIS a 766 PHE 0.024 0.002 PHE a 536 TYR 0.024 0.002 TYR a 459 ARG 0.011 0.001 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 485 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 393 PHE cc_start: 0.7998 (t80) cc_final: 0.7737 (t80) REVERT: c 449 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: b 92 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6130 (mp) REVERT: d 101 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.5570 (t80) REVERT: d 191 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6323 (t80) REVERT: f 25 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6847 (ttt) REVERT: g 10 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.5475 (m-80) REVERT: g 47 MET cc_start: 0.7353 (tpp) cc_final: 0.7069 (tpp) REVERT: g 112 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5479 (mp) REVERT: g 139 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6152 (tm-30) REVERT: h 110 ILE cc_start: 0.6295 (mt) cc_final: 0.5863 (pt) REVERT: h 128 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.5861 (t80) REVERT: h 136 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7777 (tt) REVERT: i 17 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5931 (mtt) REVERT: i 54 LYS cc_start: 0.7182 (mmtt) cc_final: 0.6536 (mmmt) REVERT: j 108 PHE cc_start: 0.4937 (OUTLIER) cc_final: 0.4620 (m-80) REVERT: k 108 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: l 17 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.5608 (ttp) REVERT: l 23 MET cc_start: 0.6832 (tpt) cc_final: 0.6536 (tpt) REVERT: m 48 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8547 (mmm-85) REVERT: n 17 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6864 (ttp) REVERT: o 47 MET cc_start: 0.8475 (tmm) cc_final: 0.7803 (tmm) REVERT: o 131 MET cc_start: 0.6546 (ttp) cc_final: 0.6258 (tmm) REVERT: e 59 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: a 59 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8146 (pt0) REVERT: a 74 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8642 (pttp) REVERT: a 101 PHE cc_start: 0.6619 (m-10) cc_final: 0.6004 (m-10) REVERT: a 188 TRP cc_start: 0.8266 (t60) cc_final: 0.7968 (t-100) REVERT: a 395 THR cc_start: 0.8039 (m) cc_final: 0.7813 (p) REVERT: a 406 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: a 475 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6241 (p90) REVERT: a 571 PHE cc_start: 0.7240 (m-80) cc_final: 0.6937 (m-80) REVERT: a 580 MET cc_start: 0.8049 (tpp) cc_final: 0.7713 (tpp) REVERT: a 752 LEU cc_start: 0.7985 (mt) cc_final: 0.7681 (mt) REVERT: a 759 MET cc_start: 0.7034 (ptt) cc_final: 0.5559 (tmm) outliers start: 216 outliers final: 161 residues processed: 624 average time/residue: 0.3612 time to fit residues: 361.7438 Evaluate side-chains 632 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 454 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 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 440 ILE Chi-restraints excluded: chain c residue 447 ASP Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 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 150 LEU Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 197 LEU 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 227 ILE Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 26 LEU 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 72 VAL Chi-restraints excluded: chain g residue 101 LEU 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 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 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 136 ILE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 17 MET Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 52 ILE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 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 89 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 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 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 51 LEU Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 151 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 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 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 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 7 ASN Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 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 59 GLN Chi-restraints excluded: chain e residue 73 ILE 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 310 CYS Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 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 763 ILE Chi-restraints excluded: chain a residue 779 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 4 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 297 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 292 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 376 ASN ** 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** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 524 ASN a 637 GLN a 766 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.154342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129110 restraints weight = 45007.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132470 restraints weight = 21669.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134552 restraints weight = 12930.145| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 24030 Z= 0.424 Angle : 0.832 11.527 32572 Z= 0.429 Chirality : 0.048 0.500 3837 Planarity : 0.005 0.072 4040 Dihedral : 8.588 105.640 3542 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 10.49 % Allowed : 22.49 % Favored : 67.02 % 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: -0.44 (0.15), residues: 3030 helix: 0.53 (0.11), residues: 2147 sheet: -0.56 (0.73), residues: 45 loop : -2.39 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP a 293 HIS 0.006 0.001 HIS a 766 PHE 0.028 0.003 PHE c 433 TYR 0.036 0.003 TYR l 144 ARG 0.013 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 728 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 259 poor density : 469 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 393 PHE cc_start: 0.8167 (t80) cc_final: 0.7945 (t80) REVERT: c 449 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: d 34 ASP cc_start: 0.8009 (m-30) cc_final: 0.7267 (m-30) REVERT: d 101 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.5705 (t80) REVERT: d 191 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.6479 (t80) REVERT: f 25 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6978 (ttt) REVERT: g 10 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.5715 (m-80) REVERT: g 47 MET cc_start: 0.7327 (tpp) cc_final: 0.7044 (tpp) REVERT: g 112 ILE cc_start: 0.5796 (OUTLIER) cc_final: 0.5578 (mp) REVERT: g 123 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.5776 (mp10) REVERT: h 44 MET cc_start: 0.5622 (ptp) cc_final: 0.5389 (ptp) REVERT: h 110 ILE cc_start: 0.6204 (mt) cc_final: 0.5753 (pt) REVERT: h 136 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7834 (tt) REVERT: i 54 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6585 (mmmt) REVERT: i 87 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.5204 (t80) REVERT: j 9 GLU cc_start: 0.6447 (mm-30) cc_final: 0.6182 (mm-30) REVERT: j 108 PHE cc_start: 0.5145 (OUTLIER) cc_final: 0.4739 (m-80) REVERT: k 108 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: l 23 MET cc_start: 0.6773 (tpt) cc_final: 0.6458 (tpt) REVERT: l 47 MET cc_start: 0.7495 (pmm) cc_final: 0.6608 (pmm) REVERT: m 48 ARG cc_start: 0.8759 (mmm160) cc_final: 0.8515 (mmm-85) REVERT: m 61 MET cc_start: 0.7067 (mmt) cc_final: 0.6538 (mmt) REVERT: n 17 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.6919 (ttp) REVERT: o 47 MET cc_start: 0.8427 (tmm) cc_final: 0.7843 (tmm) REVERT: e 63 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7431 (mm) REVERT: a 59 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8179 (pt0) REVERT: a 62 ASP cc_start: 0.8482 (m-30) cc_final: 0.8245 (m-30) REVERT: a 74 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8661 (pttp) REVERT: a 94 MET cc_start: 0.7654 (pmm) cc_final: 0.7403 (pmm) REVERT: a 277 ASP cc_start: 0.8268 (m-30) cc_final: 0.7634 (t0) REVERT: a 395 THR cc_start: 0.8035 (m) cc_final: 0.7813 (p) REVERT: a 406 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8021 (mtp) REVERT: a 475 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6395 (p90) REVERT: a 752 LEU cc_start: 0.8003 (mt) cc_final: 0.7682 (mt) REVERT: a 759 MET cc_start: 0.6972 (ptt) cc_final: 0.5566 (tmm) REVERT: a 786 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7127 (tp) outliers start: 259 outliers final: 198 residues processed: 650 average time/residue: 0.3275 time to fit residues: 344.6276 Evaluate side-chains 663 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 449 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 261 ILE 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 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 364 HIS 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 440 ILE Chi-restraints excluded: chain c residue 447 ASP Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 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 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 175 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 b residue 197 LEU 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 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 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 326 GLN 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 47 THR Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 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 108 PHE Chi-restraints excluded: chain h residue 113 VAL 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 20 SER 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 89 SER 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 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 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 143 LEU Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 150 LEU 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 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 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 28 MET 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 140 VAL Chi-restraints excluded: chain o residue 7 ASN Chi-restraints excluded: chain o residue 16 VAL Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 607 LEU Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 620 ILE Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 56 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 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 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 475 PHE Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 569 ILE Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 648 VAL Chi-restraints excluded: chain a residue 657 LEU Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 726 ILE Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 786 LEU Chi-restraints excluded: chain a residue 806 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 222 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 376 ASN c 392 ASN ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 313 HIS ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.161817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.136702 restraints weight = 44382.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140274 restraints weight = 20920.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.142542 restraints weight = 12341.007| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3392 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= 0.216 Angle : 0.691 9.467 32572 Z= 0.350 Chirality : 0.042 0.470 3837 Planarity : 0.005 0.060 4040 Dihedral : 7.986 103.580 3540 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 5.27 % Allowed : 27.47 % Favored : 67.26 % 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: 0.38 (0.15), residues: 3030 helix: 1.20 (0.11), residues: 2144 sheet: -0.72 (0.65), residues: 56 loop : -2.24 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP a 293 HIS 0.003 0.001 HIS c 438 PHE 0.027 0.002 PHE a 101 TYR 0.023 0.002 TYR l 144 ARG 0.010 0.001 ARG n 119 *********************** 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 627 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 497 time to evaluate : 2.728 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 393 PHE cc_start: 0.8073 (t80) cc_final: 0.7869 (t80) REVERT: c 447 ASP cc_start: 0.7680 (t70) cc_final: 0.6671 (p0) REVERT: c 449 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: b 68 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.8023 (t60) REVERT: d 191 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.6496 (t80) REVERT: g 10 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.5311 (m-80) REVERT: g 17 MET cc_start: 0.6397 (ttp) cc_final: 0.5772 (tpt) REVERT: g 47 MET cc_start: 0.7468 (tpp) cc_final: 0.7115 (tpp) REVERT: g 119 ARG cc_start: 0.5720 (ttm170) cc_final: 0.5273 (tpp80) REVERT: g 123 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.5707 (mp10) REVERT: h 41 ILE cc_start: 0.5463 (pt) cc_final: 0.5194 (tt) REVERT: h 110 ILE cc_start: 0.6242 (mt) cc_final: 0.5779 (pt) REVERT: h 144 TYR cc_start: 0.6536 (m-10) cc_final: 0.6087 (m-10) REVERT: i 54 LYS cc_start: 0.7174 (mmtt) cc_final: 0.6568 (mmmt) REVERT: i 139 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: j 108 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.4926 (m-80) REVERT: k 44 MET cc_start: 0.8353 (tmm) cc_final: 0.6950 (ppp) REVERT: k 108 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.6096 (m-80) REVERT: l 23 MET cc_start: 0.6755 (tpt) cc_final: 0.6392 (tpt) REVERT: l 52 ILE cc_start: 0.7586 (tt) cc_final: 0.7364 (mm) REVERT: l 123 GLN cc_start: 0.7876 (pp30) cc_final: 0.7233 (pt0) REVERT: m 61 MET cc_start: 0.6935 (mmt) cc_final: 0.6504 (mmt) REVERT: n 17 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6886 (tmm) REVERT: n 23 MET cc_start: 0.8076 (tpp) cc_final: 0.7852 (tpt) REVERT: o 47 MET cc_start: 0.8495 (tmm) cc_final: 0.7876 (tmm) REVERT: p 636 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7319 (pt) REVERT: a 59 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8142 (pt0) REVERT: a 62 ASP cc_start: 0.8349 (m-30) cc_final: 0.8110 (m-30) REVERT: a 74 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8623 (pttp) REVERT: a 94 MET cc_start: 0.7650 (pmm) cc_final: 0.7383 (pmm) REVERT: a 188 TRP cc_start: 0.7098 (t-100) cc_final: 0.6846 (t-100) REVERT: a 277 ASP cc_start: 0.8205 (m-30) cc_final: 0.7603 (t0) REVERT: a 395 THR cc_start: 0.8021 (m) cc_final: 0.7794 (p) REVERT: a 406 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: a 453 MET cc_start: 0.8136 (mtp) cc_final: 0.7654 (mtp) REVERT: a 475 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.6215 (p90) REVERT: a 571 PHE cc_start: 0.7184 (m-80) cc_final: 0.6917 (m-80) REVERT: a 580 MET cc_start: 0.8125 (tpp) cc_final: 0.7699 (tpp) REVERT: a 752 LEU cc_start: 0.7936 (mt) cc_final: 0.7673 (mt) REVERT: a 759 MET cc_start: 0.6931 (ptt) cc_final: 0.5590 (tmm) outliers start: 130 outliers final: 94 residues processed: 583 average time/residue: 0.3406 time to fit residues: 316.0857 Evaluate side-chains 564 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 458 time to evaluate : 2.431 ------------------------------------------------------------------------------- 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 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 173 LEU 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 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER 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 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 152 LEU Chi-restraints excluded: chain i residue 20 SER 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 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 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 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 115 ASP 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 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 99 VAL Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 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 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 648 VAL Chi-restraints excluded: chain a residue 658 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 277 optimal weight: 0.8980 chunk 260 optimal weight: 20.0000 chunk 253 optimal weight: 20.0000 chunk 263 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 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** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 749 HIS a 766 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.156444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131117 restraints weight = 45111.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134527 restraints weight = 21651.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136704 restraints weight = 12935.877| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 24030 Z= 0.356 Angle : 0.793 9.634 32572 Z= 0.405 Chirality : 0.046 0.470 3837 Planarity : 0.005 0.071 4040 Dihedral : 8.142 105.232 3539 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 7.09 % Allowed : 26.90 % Favored : 66.00 % 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: -0.06 (0.15), residues: 3030 helix: 0.84 (0.11), residues: 2150 sheet: -1.12 (0.52), residues: 83 loop : -2.32 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP a 757 HIS 0.006 0.001 HIS a 766 PHE 0.025 0.002 PHE a 536 TYR 0.031 0.002 TYR a 562 ARG 0.014 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 637 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 462 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 366 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7712 (tm-30) REVERT: c 393 PHE cc_start: 0.8074 (t80) cc_final: 0.7859 (t80) REVERT: c 449 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: d 34 ASP cc_start: 0.8020 (m-30) cc_final: 0.7269 (m-30) REVERT: d 101 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.5558 (t80) REVERT: d 191 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6395 (t80) REVERT: g 10 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.5643 (m-80) REVERT: g 17 MET cc_start: 0.6300 (ttp) cc_final: 0.5602 (tpt) REVERT: g 47 MET cc_start: 0.7419 (tpp) cc_final: 0.7083 (tpp) REVERT: g 112 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.5412 (mp) REVERT: g 123 GLN cc_start: 0.6818 (OUTLIER) cc_final: 0.5663 (mp10) REVERT: h 110 ILE cc_start: 0.6310 (mt) cc_final: 0.5840 (pt) REVERT: i 54 LYS cc_start: 0.7304 (mmtt) cc_final: 0.6678 (mmmt) REVERT: i 87 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5170 (t80) REVERT: i 139 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: j 9 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6163 (mm-30) REVERT: j 108 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4873 (m-80) REVERT: k 108 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: l 23 MET cc_start: 0.6817 (tpt) cc_final: 0.6512 (tpt) REVERT: l 123 GLN cc_start: 0.7695 (pp30) cc_final: 0.7237 (pt0) REVERT: m 61 MET cc_start: 0.7033 (mmt) cc_final: 0.6594 (mmt) REVERT: n 17 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6644 (ttp) REVERT: o 47 MET cc_start: 0.8477 (tmm) cc_final: 0.7848 (tmm) REVERT: e 63 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7463 (mm) REVERT: a 59 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8118 (pt0) REVERT: a 62 ASP cc_start: 0.8475 (m-30) cc_final: 0.8226 (m-30) REVERT: a 74 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8643 (pttp) REVERT: a 94 MET cc_start: 0.7625 (pmm) cc_final: 0.7314 (pmm) REVERT: a 188 TRP cc_start: 0.7264 (t-100) cc_final: 0.6911 (t-100) REVERT: a 277 ASP cc_start: 0.8310 (m-30) cc_final: 0.7594 (t0) REVERT: a 395 THR cc_start: 0.8028 (m) cc_final: 0.7811 (p) REVERT: a 406 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: a 571 PHE cc_start: 0.7319 (m-80) cc_final: 0.7049 (m-80) REVERT: a 580 MET cc_start: 0.8257 (tpp) cc_final: 0.7717 (tpp) REVERT: a 752 LEU cc_start: 0.7947 (mt) cc_final: 0.7641 (mt) REVERT: a 759 MET cc_start: 0.6980 (ptt) cc_final: 0.5679 (tmm) outliers start: 175 outliers final: 139 residues processed: 581 average time/residue: 0.3328 time to fit residues: 311.9692 Evaluate side-chains 596 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 444 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 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 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 154 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 101 PHE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 205 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 326 GLN Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 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 61 MET Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 121 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 64 ILE Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 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 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 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain k residue 17 MET Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain k residue 151 ILE Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 46 VAL 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 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 52 ILE 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 o residue 7 ASN Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 64 ILE Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 607 LEU Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 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 123 LEU Chi-restraints excluded: chain a residue 125 LEU 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 367 THR 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 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 730 LEU Chi-restraints excluded: chain a residue 763 ILE Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 791 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 112 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 330 ASN ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.161719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136670 restraints weight = 44159.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140253 restraints weight = 20915.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142499 restraints weight = 12321.168| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24030 Z= 0.221 Angle : 0.710 9.639 32572 Z= 0.357 Chirality : 0.043 0.456 3837 Planarity : 0.005 0.066 4040 Dihedral : 7.786 102.261 3539 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 5.23 % Allowed : 28.73 % Favored : 66.05 % 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: 1.24 (0.11), residues: 2139 sheet: -0.76 (0.65), residues: 56 loop : -2.24 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP a 757 HIS 0.008 0.001 HIS a 766 PHE 0.020 0.001 PHE a 475 TYR 0.029 0.002 TYR a 562 ARG 0.012 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 604 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 475 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 447 ASP cc_start: 0.7691 (t70) cc_final: 0.6621 (p0) REVERT: c 449 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: b 68 TRP cc_start: 0.8540 (OUTLIER) cc_final: 0.7899 (t60) REVERT: b 90 LYS cc_start: 0.8858 (mttm) cc_final: 0.8592 (mttp) REVERT: d 191 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.6461 (t80) REVERT: g 10 TYR cc_start: 0.6504 (OUTLIER) cc_final: 0.5507 (m-80) REVERT: g 17 MET cc_start: 0.6292 (ttp) cc_final: 0.5814 (tpt) REVERT: g 47 MET cc_start: 0.7349 (tpp) cc_final: 0.7012 (tpp) REVERT: g 112 ILE cc_start: 0.5493 (OUTLIER) cc_final: 0.5203 (mp) REVERT: g 119 ARG cc_start: 0.5710 (ttm170) cc_final: 0.5277 (tpp80) REVERT: g 123 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.5539 (mp10) REVERT: h 41 ILE cc_start: 0.5638 (pt) cc_final: 0.5331 (tt) REVERT: h 110 ILE cc_start: 0.6181 (mt) cc_final: 0.5743 (pt) REVERT: h 144 TYR cc_start: 0.6497 (m-10) cc_final: 0.6038 (m-10) REVERT: i 48 ARG cc_start: 0.7525 (mmp-170) cc_final: 0.7300 (mmm160) REVERT: i 54 LYS cc_start: 0.7163 (mmtt) cc_final: 0.6581 (mmmt) REVERT: i 139 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: j 9 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6129 (mm-30) REVERT: j 17 MET cc_start: 0.7073 (ttt) cc_final: 0.6801 (ttm) REVERT: j 108 PHE cc_start: 0.5307 (OUTLIER) cc_final: 0.4942 (m-80) REVERT: k 44 MET cc_start: 0.8377 (tmm) cc_final: 0.6892 (ppp) REVERT: k 108 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: l 17 MET cc_start: 0.5647 (mmt) cc_final: 0.4877 (ptm) REVERT: l 23 MET cc_start: 0.6787 (tpt) cc_final: 0.6432 (tpt) REVERT: l 48 ARG cc_start: 0.6919 (ptp-170) cc_final: 0.6425 (mtm180) REVERT: l 123 GLN cc_start: 0.7623 (pp30) cc_final: 0.7096 (pt0) REVERT: m 61 MET cc_start: 0.7088 (mmt) cc_final: 0.6701 (mmt) REVERT: o 47 MET cc_start: 0.8485 (tmm) cc_final: 0.7852 (tmm) REVERT: o 126 ARG cc_start: 0.8369 (mtp180) cc_final: 0.7902 (ttm170) REVERT: p 636 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7248 (pt) REVERT: a 59 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8158 (pt0) REVERT: a 62 ASP cc_start: 0.8373 (m-30) cc_final: 0.8130 (m-30) REVERT: a 74 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8681 (pttp) REVERT: a 94 MET cc_start: 0.7620 (pmm) cc_final: 0.7300 (pmm) REVERT: a 188 TRP cc_start: 0.7151 (t-100) cc_final: 0.6845 (t-100) REVERT: a 272 LEU cc_start: 0.9262 (mm) cc_final: 0.9060 (mp) REVERT: a 277 ASP cc_start: 0.8265 (m-30) cc_final: 0.7613 (t0) REVERT: a 395 THR cc_start: 0.8042 (m) cc_final: 0.7806 (p) REVERT: a 406 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7950 (mtp) REVERT: a 475 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.6157 (p90) REVERT: a 571 PHE cc_start: 0.7218 (m-80) cc_final: 0.7000 (m-80) REVERT: a 580 MET cc_start: 0.8119 (tpp) cc_final: 0.7656 (tpp) REVERT: a 665 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7798 (mmm160) REVERT: a 752 LEU cc_start: 0.7932 (mt) cc_final: 0.7619 (mp) REVERT: a 759 MET cc_start: 0.6940 (ptt) cc_final: 0.5707 (tmm) outliers start: 129 outliers final: 99 residues processed: 559 average time/residue: 0.3404 time to fit residues: 302.9684 Evaluate side-chains 570 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 459 time to evaluate : 2.548 ------------------------------------------------------------------------------- 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 14 VAL Chi-restraints excluded: chain b residue 27 TYR 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 173 LEU 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 214 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 47 THR 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 110 ILE Chi-restraints excluded: chain g residue 112 ILE 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 h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER 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 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 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 57 ILE Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 26 SER 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 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU 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 367 THR 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 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 648 VAL Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 730 LEU 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 234 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** j 124 GLN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 ASN ** a 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.160940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135816 restraints weight = 44358.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.139346 restraints weight = 21077.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.141591 restraints weight = 12498.724| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3705 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= 0.238 Angle : 0.726 16.212 32572 Z= 0.362 Chirality : 0.043 0.449 3837 Planarity : 0.005 0.067 4040 Dihedral : 7.715 101.839 3536 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 4.82 % Allowed : 29.29 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3030 helix: 1.24 (0.11), residues: 2142 sheet: -0.39 (0.73), residues: 47 loop : -2.22 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP a 757 HIS 0.009 0.001 HIS a 766 PHE 0.019 0.002 PHE a 475 TYR 0.031 0.002 TYR p 624 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 580 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 461 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 447 ASP cc_start: 0.7696 (t70) cc_final: 0.6627 (p0) REVERT: c 449 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: b 90 LYS cc_start: 0.8907 (mttm) cc_final: 0.8631 (mttp) REVERT: d 80 MET cc_start: 0.8185 (tmm) cc_final: 0.7880 (ttt) REVERT: d 191 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.6431 (t80) REVERT: g 10 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5323 (m-80) REVERT: g 17 MET cc_start: 0.6173 (ttp) cc_final: 0.5778 (tpt) REVERT: g 47 MET cc_start: 0.7317 (tpp) cc_final: 0.6998 (tpp) REVERT: g 112 ILE cc_start: 0.5504 (OUTLIER) cc_final: 0.5230 (mp) REVERT: g 119 ARG cc_start: 0.5726 (ttm170) cc_final: 0.5300 (tpp80) REVERT: g 123 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.5545 (mp10) REVERT: h 41 ILE cc_start: 0.5694 (pt) cc_final: 0.5389 (tt) REVERT: h 110 ILE cc_start: 0.6263 (mt) cc_final: 0.5804 (pt) REVERT: h 144 TYR cc_start: 0.6520 (m-10) cc_final: 0.6075 (m-10) REVERT: i 48 ARG cc_start: 0.7432 (mmp-170) cc_final: 0.7183 (mmm160) REVERT: i 54 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6609 (mmmt) REVERT: i 139 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: j 9 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6162 (mm-30) REVERT: j 17 MET cc_start: 0.7089 (ttt) cc_final: 0.6818 (ttm) REVERT: j 108 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.5033 (m-80) REVERT: k 44 MET cc_start: 0.8342 (tmm) cc_final: 0.6882 (ppp) REVERT: k 108 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: l 17 MET cc_start: 0.5699 (mmt) cc_final: 0.4948 (ptm) REVERT: l 23 MET cc_start: 0.6733 (tpt) cc_final: 0.6321 (tpt) REVERT: l 48 ARG cc_start: 0.6877 (ptp-170) cc_final: 0.6414 (mtm180) REVERT: l 123 GLN cc_start: 0.7704 (pp30) cc_final: 0.7158 (pt0) REVERT: m 48 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8153 (mtm180) REVERT: m 61 MET cc_start: 0.7066 (mmt) cc_final: 0.6676 (mmt) REVERT: n 84 ILE cc_start: 0.8176 (mt) cc_final: 0.7960 (pt) REVERT: o 47 MET cc_start: 0.8480 (tmm) cc_final: 0.8056 (tmm) REVERT: o 127 LEU cc_start: 0.8032 (tt) cc_final: 0.7817 (tt) REVERT: p 636 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7216 (pt) REVERT: a 59 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8274 (pt0) REVERT: a 62 ASP cc_start: 0.8374 (m-30) cc_final: 0.8126 (m-30) REVERT: a 74 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8618 (pttp) REVERT: a 94 MET cc_start: 0.7629 (pmm) cc_final: 0.7308 (pmm) REVERT: a 277 ASP cc_start: 0.8238 (m-30) cc_final: 0.7528 (t0) REVERT: a 284 GLN cc_start: 0.8145 (mt0) cc_final: 0.7782 (mt0) REVERT: a 395 THR cc_start: 0.8043 (m) cc_final: 0.7823 (p) REVERT: a 406 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7949 (mtp) REVERT: a 423 MET cc_start: 0.7627 (tmm) cc_final: 0.7282 (tmm) REVERT: a 475 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5856 (p90) REVERT: a 571 PHE cc_start: 0.7256 (m-80) cc_final: 0.7038 (m-80) REVERT: a 580 MET cc_start: 0.8131 (tpp) cc_final: 0.7666 (tpp) REVERT: a 752 LEU cc_start: 0.7881 (mt) cc_final: 0.7572 (mp) REVERT: a 759 MET cc_start: 0.6892 (ptt) cc_final: 0.5724 (tmm) outliers start: 119 outliers final: 103 residues processed: 541 average time/residue: 0.3498 time to fit residues: 303.2243 Evaluate side-chains 569 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 455 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 14 VAL Chi-restraints excluded: chain b residue 27 TYR 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 173 LEU 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 214 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER 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 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 h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER 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 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 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 124 GLN Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 17 MET Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 26 SER 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 150 LEU Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE 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 71 GLU Chi-restraints excluded: chain a residue 125 LEU 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 367 THR 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 455 LEU 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 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 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 20 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** j 124 GLN o 123 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.162774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.137853 restraints weight = 44189.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141442 restraints weight = 20866.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.143721 restraints weight = 12292.864| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24030 Z= 0.213 Angle : 0.720 17.768 32572 Z= 0.355 Chirality : 0.043 0.440 3837 Planarity : 0.005 0.064 4040 Dihedral : 7.557 99.746 3536 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 4.42 % Allowed : 29.38 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 3030 helix: 1.37 (0.11), residues: 2142 sheet: -0.62 (0.66), residues: 56 loop : -2.22 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP a 757 HIS 0.009 0.001 HIS a 766 PHE 0.020 0.001 PHE m 90 TYR 0.028 0.001 TYR p 624 ARG 0.014 0.001 ARG n 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7778.91 seconds wall clock time: 141 minutes 2.10 seconds (8462.10 seconds total)