Starting phenix.real_space_refine on Fri Sep 19 04:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bry_44845/09_2025/9bry_44845.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bry_44845/09_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_44845/09_2025/9bry_44845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bry_44845/09_2025/9bry_44845.map" model { file = "/net/cci-nas-00/data/ceres_data/9bry_44845/09_2025/9bry_44845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bry_44845/09_2025/9bry_44845.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.06, per 1000 atoms: 0.22 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: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.59 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: 3.96 Time building geometry restraints manager: 2.72 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.090 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- 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 24041 Z= 0.233 Angle : 0.893 15.550 32605 Z= 0.477 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 : 5.04 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG a 264 TYR 0.045 0.002 TYR a 459 PHE 0.030 0.002 PHE a 777 TRP 0.021 0.001 TRP a 293 HIS 0.008 0.001 HIS c 364 Details of bonding type rmsd covalent geometry : bond 0.00470 (24030) covalent geometry : angle 0.87602 (32572) hydrogen bonds : bond 0.17063 ( 1688) hydrogen bonds : angle 6.56096 ( 4935) link_BETA1-4 : bond 0.01038 ( 4) link_BETA1-4 : angle 5.21085 ( 12) link_NAG-ASN : bond 0.01509 ( 7) link_NAG-ASN : angle 5.65802 ( 21) *********************** 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 : 0.786 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: 0.6352 (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: 0.7107 (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: 0.6030 (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: 0.7147 (ppp) REVERT: k 108 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5914 (m-80) REVERT: l 23 MET cc_start: 0.6262 (tpt) cc_final: 0.6029 (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: 0.6345 (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: 0.8428 (mt-10) REVERT: a 70 LYS cc_start: 0.9377 (tppt) cc_final: 0.8831 (ptpt) 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: 0.1558 time to fit residues: 154.6420 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 : 0.876 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.163865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.138320 restraints weight = 43770.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142016 restraints weight = 20820.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.144370 restraints weight = 12281.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.145775 restraints weight = 8586.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.146741 restraints weight = 6866.710| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24041 Z= 0.190 Angle : 0.714 11.417 32605 Z= 0.364 Chirality : 0.044 0.490 3837 Planarity : 0.005 0.058 4040 Dihedral : 8.751 113.978 3607 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 5.23 % Allowed : 18.52 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3030 helix: 1.35 (0.11), residues: 2112 sheet: -0.58 (0.58), residues: 68 loop : -1.77 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG a 264 TYR 0.034 0.002 TYR a 459 PHE 0.019 0.002 PHE g 128 TRP 0.019 0.002 TRP a 293 HIS 0.016 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00392 (24030) covalent geometry : angle 0.70058 (32572) hydrogen bonds : bond 0.07471 ( 1688) hydrogen bonds : angle 4.86169 ( 4935) link_BETA1-4 : bond 0.01225 ( 4) link_BETA1-4 : angle 4.79408 ( 12) link_NAG-ASN : bond 0.00601 ( 7) link_NAG-ASN : angle 4.03149 ( 21) *********************** 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 671 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 542 time to evaluate : 0.637 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: 0.7322 (t70) cc_final: 0.6415 (p0) REVERT: c 448 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7444 (ttm110) REVERT: c 449 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6619 (m-80) REVERT: b 204 MET cc_start: 0.7470 (ttp) cc_final: 0.7258 (ttm) REVERT: d 139 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6291 (pm20) REVERT: d 191 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.6260 (t80) REVERT: g 17 MET cc_start: 0.6255 (ttm) cc_final: 0.5973 (tpt) REVERT: h 41 ILE cc_start: 0.5943 (pt) cc_final: 0.5604 (tt) REVERT: h 110 ILE cc_start: 0.6336 (mt) cc_final: 0.5946 (pt) REVERT: h 128 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6557 (t80) REVERT: h 136 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7508 (tt) REVERT: i 54 LYS cc_start: 0.7149 (mmtt) cc_final: 0.6411 (mmmt) REVERT: i 131 MET cc_start: 0.5775 (ttp) cc_final: 0.5416 (ttp) REVERT: j 44 MET cc_start: 0.5965 (tmm) cc_final: 0.5681 (tmm) REVERT: j 108 PHE cc_start: 0.4477 (OUTLIER) cc_final: 0.4182 (m-80) REVERT: j 133 LEU cc_start: 0.5118 (tp) cc_final: 0.4911 (tt) REVERT: k 44 MET cc_start: 0.7844 (tmm) cc_final: 0.7288 (ppp) REVERT: k 57 ILE cc_start: 0.8108 (mm) cc_final: 0.7882 (mp) REVERT: k 108 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: l 47 MET cc_start: 0.7208 (pmm) cc_final: 0.6264 (pmm) REVERT: l 124 GLN cc_start: 0.7326 (tp-100) cc_final: 0.6555 (tm-30) REVERT: m 7 ASN cc_start: 0.5992 (m-40) cc_final: 0.5633 (p0) REVERT: m 48 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8469 (mmm-85) REVERT: n 61 MET cc_start: 0.6040 (mmt) cc_final: 0.5654 (mmt) REVERT: o 47 MET cc_start: 0.8473 (tmm) cc_final: 0.7916 (tmm) REVERT: a 11 THR cc_start: 0.4813 (OUTLIER) cc_final: 0.4459 (p) REVERT: a 74 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8654 (pttp) REVERT: a 179 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6629 (mtm180) REVERT: a 188 TRP cc_start: 0.7838 (t60) cc_final: 0.7345 (t-100) REVERT: a 257 MET cc_start: 0.7819 (ptp) cc_final: 0.7609 (ptt) REVERT: a 298 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7992 (mmt90) REVERT: a 395 THR cc_start: 0.8064 (m) cc_final: 0.7845 (p) REVERT: a 399 PHE cc_start: 0.7276 (t80) cc_final: 0.6998 (t80) REVERT: a 406 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7964 (mtp) REVERT: a 453 MET cc_start: 0.8308 (mtp) cc_final: 0.7770 (mtp) REVERT: a 752 LEU cc_start: 0.8085 (mt) cc_final: 0.7771 (mt) REVERT: a 759 MET cc_start: 0.6848 (ptt) cc_final: 0.5550 (tmm) outliers start: 129 outliers final: 81 residues processed: 617 average time/residue: 0.1482 time to fit residues: 146.2432 Evaluate side-chains 580 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 489 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 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 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 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 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 121 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 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 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 12 ILE Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 48 CYS Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 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 192 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 300 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 376 ASN ** 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 559 ASN a 766 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.157480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131975 restraints weight = 44781.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.135462 restraints weight = 21702.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137708 restraints weight = 12947.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139132 restraints weight = 9102.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139912 restraints weight = 7239.668| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 24041 Z= 0.250 Angle : 0.794 12.189 32605 Z= 0.404 Chirality : 0.047 0.471 3837 Planarity : 0.005 0.082 4040 Dihedral : 8.499 110.390 3546 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 8.27 % Allowed : 19.49 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.15), residues: 3030 helix: 0.90 (0.11), residues: 2125 sheet: -0.38 (0.64), residues: 58 loop : -2.07 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG n 119 TYR 0.024 0.002 TYR b 71 PHE 0.030 0.003 PHE a 67 TRP 0.022 0.002 TRP c 333 HIS 0.011 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00563 (24030) covalent geometry : angle 0.78097 (32572) hydrogen bonds : bond 0.07928 ( 1688) hydrogen bonds : angle 4.99870 ( 4935) link_BETA1-4 : bond 0.01094 ( 4) link_BETA1-4 : angle 4.77565 ( 12) link_NAG-ASN : bond 0.00736 ( 7) link_NAG-ASN : angle 4.32606 ( 21) *********************** 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 711 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 507 time to evaluate : 0.842 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 449 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: d 34 ASP cc_start: 0.8052 (m-30) cc_final: 0.7344 (m-30) REVERT: d 191 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.6364 (t80) REVERT: f 25 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6860 (ttt) REVERT: f 42 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7781 (mt-10) REVERT: g 10 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.5508 (m-80) REVERT: h 23 MET cc_start: 0.5174 (tpt) cc_final: 0.4816 (tpt) REVERT: h 110 ILE cc_start: 0.6397 (mt) cc_final: 0.5937 (pt) REVERT: h 128 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6402 (t80) REVERT: h 136 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7781 (tt) REVERT: i 36 LYS cc_start: 0.5595 (OUTLIER) cc_final: 0.5319 (tppp) REVERT: i 54 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6462 (mmmt) REVERT: j 108 PHE cc_start: 0.4826 (OUTLIER) cc_final: 0.4396 (m-80) REVERT: k 108 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.6240 (m-80) REVERT: l 47 MET cc_start: 0.7313 (pmm) cc_final: 0.6496 (pmm) REVERT: l 124 GLN cc_start: 0.7444 (tp-100) cc_final: 0.6418 (tm-30) REVERT: m 48 ARG cc_start: 0.8709 (mmm160) cc_final: 0.8402 (mmm-85) REVERT: n 17 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6876 (ttp) REVERT: o 47 MET cc_start: 0.8482 (tmm) cc_final: 0.7903 (tmm) REVERT: a 11 THR cc_start: 0.4693 (OUTLIER) cc_final: 0.4386 (p) REVERT: a 74 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8632 (pttm) REVERT: a 188 TRP cc_start: 0.8108 (t60) cc_final: 0.7677 (t-100) REVERT: a 277 ASP cc_start: 0.8288 (m-30) cc_final: 0.7797 (t0) REVERT: a 395 THR cc_start: 0.8058 (m) cc_final: 0.7821 (p) REVERT: a 406 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8017 (mtp) REVERT: a 453 MET cc_start: 0.8260 (mtp) cc_final: 0.8025 (mtp) REVERT: a 467 CYS cc_start: 0.6960 (t) cc_final: 0.6423 (p) REVERT: a 475 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6534 (p90) REVERT: a 752 LEU cc_start: 0.8080 (mt) cc_final: 0.7783 (mt) REVERT: a 759 MET cc_start: 0.7063 (ptt) cc_final: 0.5822 (tmm) outliers start: 204 outliers final: 138 residues processed: 641 average time/residue: 0.1419 time to fit residues: 147.7387 Evaluate side-chains 613 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 462 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 356 THR Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 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 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 101 LEU Chi-restraints excluded: chain g residue 148 VAL Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 113 VAL Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 36 LYS Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 136 ILE Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 44 MET Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 136 ILE Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 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 p residue 592 ASN Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 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 334 GLN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 450 ILE Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 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 643 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 763 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 182 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 298 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 295 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 376 ASN d 342 HIS ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.160841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.135474 restraints weight = 44436.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.139020 restraints weight = 21255.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.141319 restraints weight = 12611.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.142623 restraints weight = 8856.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143539 restraints weight = 7148.359| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24041 Z= 0.173 Angle : 0.693 11.657 32605 Z= 0.349 Chirality : 0.043 0.485 3837 Planarity : 0.005 0.064 4040 Dihedral : 8.161 106.586 3543 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 7.09 % Allowed : 21.64 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.15), residues: 3030 helix: 1.25 (0.11), residues: 2128 sheet: -0.54 (0.56), residues: 78 loop : -1.98 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG n 119 TYR 0.019 0.001 TYR l 87 PHE 0.024 0.002 PHE b 174 TRP 0.027 0.002 TRP a 757 HIS 0.006 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00368 (24030) covalent geometry : angle 0.67949 (32572) hydrogen bonds : bond 0.06811 ( 1688) hydrogen bonds : angle 4.57787 ( 4935) link_BETA1-4 : bond 0.01150 ( 4) link_BETA1-4 : angle 4.89559 ( 12) link_NAG-ASN : bond 0.00630 ( 7) link_NAG-ASN : angle 4.00258 ( 21) *********************** 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 678 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 503 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 447 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.6554 (p0) REVERT: c 449 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: d 191 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.6349 (t80) REVERT: f 25 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6774 (ttt) REVERT: f 42 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7764 (mt-10) REVERT: g 119 ARG cc_start: 0.5945 (ttm170) cc_final: 0.5679 (tpp80) REVERT: g 123 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.5660 (mp10) REVERT: h 23 MET cc_start: 0.4928 (tpt) cc_final: 0.4642 (tpt) REVERT: h 44 MET cc_start: 0.5367 (ptp) cc_final: 0.5166 (ptp) REVERT: h 110 ILE cc_start: 0.6237 (mt) cc_final: 0.5822 (pt) REVERT: h 128 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6078 (t80) REVERT: h 136 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7703 (tt) REVERT: i 54 LYS cc_start: 0.7070 (mmtt) cc_final: 0.6449 (mmmt) REVERT: j 108 PHE cc_start: 0.4745 (OUTLIER) cc_final: 0.4395 (m-80) REVERT: k 44 MET cc_start: 0.8209 (tmm) cc_final: 0.6969 (ppp) REVERT: k 108 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.6172 (m-80) REVERT: l 17 MET cc_start: 0.6656 (mmp) cc_final: 0.5557 (ttp) REVERT: l 23 MET cc_start: 0.6395 (tpt) cc_final: 0.6108 (tpt) REVERT: l 47 MET cc_start: 0.7139 (pmm) cc_final: 0.6899 (pmm) REVERT: l 124 GLN cc_start: 0.7415 (tp-100) cc_final: 0.6412 (tm-30) REVERT: m 48 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8485 (mmm-85) REVERT: n 17 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6892 (ttp) REVERT: o 47 MET cc_start: 0.8469 (tmm) cc_final: 0.7872 (tmm) REVERT: e 59 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7164 (mt0) REVERT: e 63 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7323 (mm) REVERT: a 59 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8749 (mm-30) REVERT: a 74 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8594 (pttp) REVERT: a 277 ASP cc_start: 0.8322 (m-30) cc_final: 0.7792 (t0) REVERT: a 395 THR cc_start: 0.8043 (m) cc_final: 0.7799 (p) REVERT: a 406 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7975 (mtp) REVERT: a 467 CYS cc_start: 0.6810 (t) cc_final: 0.6014 (m) REVERT: a 752 LEU cc_start: 0.8092 (mt) cc_final: 0.7781 (mt) REVERT: a 759 MET cc_start: 0.6946 (ptt) cc_final: 0.5724 (tmm) outliers start: 175 outliers final: 122 residues processed: 610 average time/residue: 0.1389 time to fit residues: 136.9901 Evaluate side-chains 601 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 466 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 447 ASP Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 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 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 227 ILE Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 78 LEU 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 110 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 53 MET Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 93 LEU 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 46 VAL Chi-restraints excluded: chain i residue 52 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain j residue 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 k residue 59 VAL Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 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 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 115 ASP Chi-restraints excluded: chain m residue 121 THR 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 17 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 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 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 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 725 THR Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 206 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 524 ASN ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.159634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.134375 restraints weight = 44030.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137859 restraints weight = 21231.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140120 restraints weight = 12662.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.141406 restraints weight = 8936.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142378 restraints weight = 7231.178| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24041 Z= 0.190 Angle : 0.714 12.061 32605 Z= 0.359 Chirality : 0.044 0.460 3837 Planarity : 0.005 0.066 4040 Dihedral : 8.051 110.150 3540 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 8.51 % Allowed : 21.52 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.15), residues: 3030 helix: 1.19 (0.11), residues: 2138 sheet: -0.47 (0.72), residues: 47 loop : -2.11 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG n 119 TYR 0.018 0.002 TYR b 71 PHE 0.023 0.002 PHE b 174 TRP 0.027 0.002 TRP a 188 HIS 0.006 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00424 (24030) covalent geometry : angle 0.69958 (32572) hydrogen bonds : bond 0.06766 ( 1688) hydrogen bonds : angle 4.57648 ( 4935) link_BETA1-4 : bond 0.01153 ( 4) link_BETA1-4 : angle 4.79939 ( 12) link_NAG-ASN : bond 0.00583 ( 7) link_NAG-ASN : angle 4.34833 ( 21) *********************** 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 709 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 499 time to evaluate : 0.616 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 449 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.6755 (m-80) REVERT: b 92 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5761 (mp) REVERT: d 191 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.6337 (t80) REVERT: f 25 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6763 (ttt) REVERT: f 42 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7791 (mt-10) REVERT: g 10 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5365 (m-80) REVERT: g 17 MET cc_start: 0.6540 (ttp) cc_final: 0.5704 (tpt) REVERT: g 112 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5401 (mp) REVERT: h 110 ILE cc_start: 0.6215 (mt) cc_final: 0.5752 (pt) REVERT: h 128 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6088 (t80) REVERT: h 136 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7682 (tt) REVERT: h 144 TYR cc_start: 0.6646 (m-10) cc_final: 0.6221 (m-10) REVERT: i 54 LYS cc_start: 0.7098 (mmtt) cc_final: 0.6459 (mmmt) REVERT: i 139 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: j 108 PHE cc_start: 0.4756 (OUTLIER) cc_final: 0.4409 (m-80) REVERT: k 44 MET cc_start: 0.8285 (tmm) cc_final: 0.7113 (ppp) REVERT: k 108 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: l 17 MET cc_start: 0.6759 (mmp) cc_final: 0.5590 (ptt) REVERT: l 23 MET cc_start: 0.6572 (tpt) cc_final: 0.6261 (tpt) REVERT: l 124 GLN cc_start: 0.7294 (tp-100) cc_final: 0.6364 (tm-30) REVERT: m 48 ARG cc_start: 0.8745 (mmm160) cc_final: 0.8541 (mmm-85) REVERT: n 17 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6849 (ttp) REVERT: o 47 MET cc_start: 0.8482 (tmm) cc_final: 0.7658 (tmm) REVERT: e 59 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: e 63 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7403 (mm) REVERT: a 59 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8091 (pt0) REVERT: a 74 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8590 (pttp) REVERT: a 277 ASP cc_start: 0.8293 (m-30) cc_final: 0.7775 (t0) REVERT: a 395 THR cc_start: 0.8037 (m) cc_final: 0.7803 (p) REVERT: a 406 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8000 (mtp) REVERT: a 467 CYS cc_start: 0.6877 (t) cc_final: 0.5996 (m) REVERT: a 580 MET cc_start: 0.7750 (tpp) cc_final: 0.7549 (tpp) REVERT: a 752 LEU cc_start: 0.8092 (mt) cc_final: 0.7785 (mt) REVERT: a 759 MET cc_start: 0.7030 (ptt) cc_final: 0.5543 (tmm) outliers start: 210 outliers final: 159 residues processed: 633 average time/residue: 0.1347 time to fit residues: 138.9307 Evaluate side-chains 640 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 466 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 288 ASN Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 43 THR Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 68 TRP Chi-restraints excluded: chain b residue 71 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 77 ILE Chi-restraints excluded: chain b residue 92 LEU Chi-restraints excluded: chain b residue 103 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 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 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain 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 93 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 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 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 84 ILE Chi-restraints excluded: chain j residue 89 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 57 ILE 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 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 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 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 112 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 108 PHE 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 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 613 ILE Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 334 GLN 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 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 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 725 THR Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 49 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 364 HIS ** c 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 392 ASN ** 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** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 473 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 = 0.4098 r_free = 0.4098 target = 0.157636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132487 restraints weight = 44693.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.135972 restraints weight = 21427.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138208 restraints weight = 12717.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139484 restraints weight = 8944.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140492 restraints weight = 7236.084| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 24041 Z= 0.216 Angle : 0.755 12.490 32605 Z= 0.381 Chirality : 0.045 0.468 3837 Planarity : 0.005 0.070 4040 Dihedral : 8.128 108.931 3540 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 9.12 % Allowed : 22.08 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3030 helix: 1.04 (0.11), residues: 2137 sheet: -1.23 (0.52), residues: 83 loop : -2.16 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG n 119 TYR 0.032 0.002 TYR l 144 PHE 0.032 0.002 PHE b 48 TRP 0.031 0.002 TRP a 757 HIS 0.006 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00489 (24030) covalent geometry : angle 0.74104 (32572) hydrogen bonds : bond 0.07114 ( 1688) hydrogen bonds : angle 4.71706 ( 4935) link_BETA1-4 : bond 0.01074 ( 4) link_BETA1-4 : angle 4.72885 ( 12) link_NAG-ASN : bond 0.00571 ( 7) link_NAG-ASN : angle 4.41248 ( 21) *********************** 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 694 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 469 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 449 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: b 92 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6277 (mp) REVERT: d 101 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.5663 (t80) REVERT: d 191 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6367 (t80) REVERT: f 25 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6827 (ttt) REVERT: g 10 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.5519 (m-80) REVERT: g 17 MET cc_start: 0.6490 (ttp) cc_final: 0.5821 (tpt) REVERT: g 112 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5356 (mp) REVERT: g 123 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.5721 (mp10) REVERT: g 139 GLU cc_start: 0.6387 (tm-30) cc_final: 0.6015 (tm-30) REVERT: h 110 ILE cc_start: 0.6315 (mt) cc_final: 0.5888 (pt) REVERT: h 128 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.5797 (t80) REVERT: h 144 TYR cc_start: 0.6746 (m-10) cc_final: 0.6243 (m-10) REVERT: i 54 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6493 (mmmt) REVERT: i 139 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: j 108 PHE cc_start: 0.5117 (OUTLIER) cc_final: 0.4727 (m-80) REVERT: k 28 MET cc_start: 0.7236 (mtp) cc_final: 0.7018 (mtp) REVERT: k 108 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: l 17 MET cc_start: 0.6830 (mmp) cc_final: 0.5578 (ttp) REVERT: l 23 MET cc_start: 0.6705 (tpt) cc_final: 0.6392 (tpt) REVERT: l 124 GLN cc_start: 0.7371 (tp-100) cc_final: 0.6413 (tm-30) REVERT: n 17 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6835 (ttp) REVERT: o 47 MET cc_start: 0.8444 (tmm) cc_final: 0.7781 (tmm) REVERT: e 63 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7402 (mm) REVERT: a 59 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8584 (mm-30) REVERT: a 62 ASP cc_start: 0.8451 (m-30) cc_final: 0.8033 (m-30) REVERT: a 74 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8632 (pttp) REVERT: a 277 ASP cc_start: 0.8276 (m-30) cc_final: 0.7713 (t0) REVERT: a 395 THR cc_start: 0.7980 (m) cc_final: 0.7764 (p) REVERT: a 406 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8002 (mtp) REVERT: a 467 CYS cc_start: 0.6969 (t) cc_final: 0.6078 (m) REVERT: a 752 LEU cc_start: 0.8002 (mt) cc_final: 0.7683 (mt) REVERT: a 759 MET cc_start: 0.7017 (ptt) cc_final: 0.5581 (tmm) outliers start: 225 outliers final: 170 residues processed: 623 average time/residue: 0.1378 time to fit residues: 139.4386 Evaluate side-chains 630 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 445 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 447 ASP Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL 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 103 ILE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 115 MET Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 182 ILE Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain 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 201 LEU Chi-restraints excluded: chain d residue 205 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 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 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 72 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain 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 93 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 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 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 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 37 SER Chi-restraints excluded: chain l residue 46 VAL 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 91 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 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 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 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 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 112 ILE Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 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 123 LEU Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 397 ILE Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 99 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 274 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 256 optimal weight: 5.9990 chunk 148 optimal weight: 0.2980 chunk 275 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 330 ASN ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 56 GLN ** 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 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.159960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.134870 restraints weight = 44148.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.138391 restraints weight = 21049.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140657 restraints weight = 12469.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142004 restraints weight = 8772.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.142967 restraints weight = 7058.123| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24041 Z= 0.174 Angle : 0.712 12.018 32605 Z= 0.356 Chirality : 0.043 0.459 3837 Planarity : 0.005 0.067 4040 Dihedral : 7.948 107.091 3540 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 7.70 % Allowed : 23.78 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3030 helix: 1.21 (0.11), residues: 2139 sheet: -0.73 (0.65), residues: 57 loop : -2.15 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG n 119 TYR 0.027 0.002 TYR l 144 PHE 0.027 0.002 PHE b 174 TRP 0.039 0.002 TRP a 293 HIS 0.007 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00382 (24030) covalent geometry : angle 0.69906 (32572) hydrogen bonds : bond 0.06484 ( 1688) hydrogen bonds : angle 4.47583 ( 4935) link_BETA1-4 : bond 0.01037 ( 4) link_BETA1-4 : angle 4.77060 ( 12) link_NAG-ASN : bond 0.00605 ( 7) link_NAG-ASN : angle 4.12241 ( 21) *********************** 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 671 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 481 time to evaluate : 0.852 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 449 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: d 101 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.5633 (t80) REVERT: d 107 MET cc_start: 0.6281 (mtp) cc_final: 0.5277 (mtp) REVERT: d 178 MET cc_start: 0.8111 (ppp) cc_final: 0.7828 (ppp) REVERT: d 191 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.6347 (t80) REVERT: f 25 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6773 (ttt) REVERT: g 10 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.5413 (m-80) REVERT: g 17 MET cc_start: 0.6394 (ttp) cc_final: 0.5796 (tpt) REVERT: g 112 ILE cc_start: 0.5451 (OUTLIER) cc_final: 0.5229 (mp) REVERT: g 123 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.5678 (mp10) REVERT: g 139 GLU cc_start: 0.6327 (tm-30) cc_final: 0.5953 (tm-30) REVERT: h 110 ILE cc_start: 0.6213 (mt) cc_final: 0.5813 (pt) REVERT: h 128 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.5768 (t80) REVERT: h 144 TYR cc_start: 0.6617 (m-10) cc_final: 0.6178 (m-10) REVERT: i 54 LYS cc_start: 0.7091 (mmtt) cc_final: 0.6492 (mmmt) REVERT: i 139 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: j 17 MET cc_start: 0.7093 (ttt) cc_final: 0.6839 (ttm) REVERT: j 108 PHE cc_start: 0.5002 (OUTLIER) cc_final: 0.4668 (m-80) REVERT: k 44 MET cc_start: 0.8321 (tmm) cc_final: 0.6943 (ppp) REVERT: k 108 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: l 17 MET cc_start: 0.6726 (mmp) cc_final: 0.5550 (ttp) REVERT: l 23 MET cc_start: 0.6641 (tpt) cc_final: 0.6258 (tpt) REVERT: l 48 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6776 (mmm160) REVERT: l 124 GLN cc_start: 0.7400 (tp-100) cc_final: 0.6523 (tm-30) REVERT: n 17 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7016 (tmm) REVERT: o 47 MET cc_start: 0.8465 (tmm) cc_final: 0.7764 (tmm) REVERT: o 126 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7801 (ttp80) REVERT: e 63 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7375 (mm) REVERT: a 59 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8643 (mm-30) REVERT: a 62 ASP cc_start: 0.8427 (m-30) cc_final: 0.8004 (m-30) REVERT: a 71 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: a 74 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8599 (pttp) REVERT: a 94 MET cc_start: 0.7196 (pmm) cc_final: 0.6987 (pmm) REVERT: a 101 PHE cc_start: 0.6753 (m-10) cc_final: 0.6493 (m-10) REVERT: a 277 ASP cc_start: 0.8227 (m-30) cc_final: 0.7678 (t0) REVERT: a 291 ARG cc_start: 0.7199 (mmp80) cc_final: 0.6784 (mmp80) REVERT: a 395 THR cc_start: 0.8021 (m) cc_final: 0.7798 (p) REVERT: a 403 PHE cc_start: 0.8230 (t80) cc_final: 0.8020 (t80) REVERT: a 406 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8002 (mtp) REVERT: a 467 CYS cc_start: 0.7061 (t) cc_final: 0.6190 (m) REVERT: a 580 MET cc_start: 0.8054 (tpp) cc_final: 0.7648 (tpp) REVERT: a 752 LEU cc_start: 0.7985 (mt) cc_final: 0.7669 (mt) REVERT: a 759 MET cc_start: 0.6947 (ptt) cc_final: 0.5565 (tmm) outliers start: 190 outliers final: 150 residues processed: 609 average time/residue: 0.1403 time to fit residues: 138.9137 Evaluate side-chains 617 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 452 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 346 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 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 103 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 155 CYS 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 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 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 132 ILE Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain 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 93 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 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 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 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 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 147 ILE 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 46 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 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 127 LEU Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU 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 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 112 ILE Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 603 VAL 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 19 LEU Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 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 334 GLN Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 485 PHE Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 535 SER Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 569 ILE Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 619 PHE Chi-restraints excluded: chain a residue 642 VAL Chi-restraints excluded: chain a residue 648 VAL Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 4 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 228 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 131 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.161040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.136025 restraints weight = 44177.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139592 restraints weight = 21101.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.141852 restraints weight = 12485.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.143156 restraints weight = 8761.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.144142 restraints weight = 7095.762| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24041 Z= 0.165 Angle : 0.713 11.764 32605 Z= 0.355 Chirality : 0.043 0.449 3837 Planarity : 0.005 0.067 4040 Dihedral : 7.805 106.226 3540 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 7.25 % Allowed : 24.72 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 3030 helix: 1.29 (0.11), residues: 2135 sheet: -0.73 (0.65), residues: 57 loop : -2.14 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG n 119 TYR 0.026 0.002 TYR l 144 PHE 0.028 0.002 PHE b 174 TRP 0.056 0.002 TRP a 293 HIS 0.008 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00361 (24030) covalent geometry : angle 0.70043 (32572) hydrogen bonds : bond 0.06148 ( 1688) hydrogen bonds : angle 4.41679 ( 4935) link_BETA1-4 : bond 0.01104 ( 4) link_BETA1-4 : angle 4.76363 ( 12) link_NAG-ASN : bond 0.00619 ( 7) link_NAG-ASN : angle 4.03865 ( 21) *********************** 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 647 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 468 time to evaluate : 0.809 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: 0.7620 (t70) cc_final: 0.6595 (p0) REVERT: c 449 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6294 (m-80) REVERT: d 101 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.5707 (t80) REVERT: d 107 MET cc_start: 0.6496 (mtp) cc_final: 0.5513 (mtp) REVERT: d 191 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.6299 (t80) REVERT: f 25 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6687 (ttt) REVERT: g 10 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5358 (m-80) REVERT: g 17 MET cc_start: 0.6345 (ttp) cc_final: 0.5796 (tpt) REVERT: g 112 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5136 (mp) REVERT: g 123 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.5621 (mp10) REVERT: h 41 ILE cc_start: 0.5755 (pt) cc_final: 0.5535 (tt) REVERT: h 110 ILE cc_start: 0.6215 (mt) cc_final: 0.5776 (pt) REVERT: h 144 TYR cc_start: 0.6508 (m-10) cc_final: 0.6045 (m-10) REVERT: i 54 LYS cc_start: 0.7074 (mmtt) cc_final: 0.6486 (mmmt) REVERT: i 139 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: j 17 MET cc_start: 0.7092 (ttt) cc_final: 0.6835 (ttm) REVERT: j 108 PHE cc_start: 0.5189 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: k 44 MET cc_start: 0.8369 (tmm) cc_final: 0.6922 (ppp) REVERT: k 108 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.6041 (m-80) REVERT: l 17 MET cc_start: 0.6663 (mmp) cc_final: 0.5566 (ttp) REVERT: l 23 MET cc_start: 0.6621 (tpt) cc_final: 0.6179 (tpt) REVERT: l 48 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6809 (mmm160) REVERT: l 124 GLN cc_start: 0.7346 (tp-100) cc_final: 0.6853 (tm-30) REVERT: m 48 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8483 (mmm-85) REVERT: n 17 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7250 (tmm) REVERT: n 23 MET cc_start: 0.8266 (tpp) cc_final: 0.8029 (tpt) REVERT: n 84 ILE cc_start: 0.8485 (mt) cc_final: 0.8185 (pt) REVERT: o 47 MET cc_start: 0.8466 (tmm) cc_final: 0.7752 (tmm) REVERT: p 636 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7277 (pt) REVERT: e 63 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7365 (mm) REVERT: a 59 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8721 (mm-30) REVERT: a 62 ASP cc_start: 0.8453 (m-30) cc_final: 0.8014 (m-30) REVERT: a 71 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: a 74 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8602 (pttp) REVERT: a 277 ASP cc_start: 0.8168 (m-30) cc_final: 0.7672 (t0) REVERT: a 291 ARG cc_start: 0.7147 (mmp80) cc_final: 0.6771 (mmp80) REVERT: a 395 THR cc_start: 0.8028 (m) cc_final: 0.7806 (p) REVERT: a 403 PHE cc_start: 0.8311 (t80) cc_final: 0.8056 (t80) REVERT: a 406 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7941 (mtp) REVERT: a 467 CYS cc_start: 0.7110 (t) cc_final: 0.6266 (m) REVERT: a 580 MET cc_start: 0.8191 (tpp) cc_final: 0.7751 (tpp) REVERT: a 752 LEU cc_start: 0.7985 (mt) cc_final: 0.7728 (mt) REVERT: a 759 MET cc_start: 0.6981 (ptt) cc_final: 0.5628 (tmm) outliers start: 179 outliers final: 146 residues processed: 591 average time/residue: 0.1366 time to fit residues: 131.6939 Evaluate side-chains 611 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 450 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 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 103 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 155 CYS 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 170 ILE Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 191 TYR Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 56 GLN Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 7 ASN Chi-restraints excluded: chain g residue 10 TYR Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 53 MET Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 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 j residue 21 SER 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 99 VAL Chi-restraints excluded: chain j residue 108 PHE Chi-restraints excluded: chain j residue 124 GLN Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 99 VAL Chi-restraints excluded: chain k residue 102 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 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 37 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER 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 112 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain 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 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 127 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 592 ASN Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 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 19 LEU Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 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 334 GLN Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 165 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 40 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 295 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 392 ASN ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 313 HIS ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 56 GLN ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN n 123 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 = 0.4143 r_free = 0.4143 target = 0.161788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.136717 restraints weight = 44227.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140270 restraints weight = 21061.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142549 restraints weight = 12456.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.143867 restraints weight = 8733.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.144844 restraints weight = 7042.303| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24041 Z= 0.161 Angle : 0.718 13.730 32605 Z= 0.355 Chirality : 0.043 0.441 3837 Planarity : 0.005 0.067 4040 Dihedral : 7.711 105.356 3540 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 6.89 % Allowed : 25.28 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 3030 helix: 1.34 (0.11), residues: 2144 sheet: -0.81 (0.52), residues: 83 loop : -2.13 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG n 119 TYR 0.041 0.002 TYR a 562 PHE 0.028 0.002 PHE b 174 TRP 0.046 0.002 TRP a 293 HIS 0.008 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00350 (24030) covalent geometry : angle 0.70529 (32572) hydrogen bonds : bond 0.05957 ( 1688) hydrogen bonds : angle 4.38254 ( 4935) link_BETA1-4 : bond 0.01087 ( 4) link_BETA1-4 : angle 4.75319 ( 12) link_NAG-ASN : bond 0.00602 ( 7) link_NAG-ASN : angle 3.96856 ( 21) *********************** 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 644 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 474 time to evaluate : 0.867 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: 0.7601 (t70) cc_final: 0.6573 (p0) REVERT: c 449 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6321 (m-80) REVERT: b 68 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.7998 (t60) REVERT: d 101 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.5705 (t80) REVERT: d 107 MET cc_start: 0.6571 (mtp) cc_final: 0.5608 (mtp) REVERT: d 191 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6292 (t80) REVERT: f 25 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6661 (ttt) REVERT: g 10 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.5335 (m-80) REVERT: g 17 MET cc_start: 0.6271 (ttp) cc_final: 0.5904 (tpt) REVERT: g 112 ILE cc_start: 0.5220 (OUTLIER) cc_final: 0.4991 (mp) REVERT: g 123 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.5585 (mp10) REVERT: h 41 ILE cc_start: 0.5739 (pt) cc_final: 0.5535 (tt) REVERT: h 110 ILE cc_start: 0.6227 (mt) cc_final: 0.5759 (pt) REVERT: i 54 LYS cc_start: 0.7066 (mmtt) cc_final: 0.6485 (mmmt) REVERT: i 139 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: j 17 MET cc_start: 0.7095 (ttt) cc_final: 0.6833 (ttm) REVERT: j 108 PHE cc_start: 0.5113 (OUTLIER) cc_final: 0.4783 (m-80) REVERT: k 44 MET cc_start: 0.8286 (tmm) cc_final: 0.6882 (ppp) REVERT: k 108 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.6016 (m-80) REVERT: l 17 MET cc_start: 0.6609 (mmp) cc_final: 0.5579 (ttp) REVERT: l 23 MET cc_start: 0.6597 (tpt) cc_final: 0.6234 (tpt) REVERT: l 48 ARG cc_start: 0.7104 (mmm160) cc_final: 0.6885 (mmm160) REVERT: l 124 GLN cc_start: 0.7544 (tp-100) cc_final: 0.6773 (tm-30) REVERT: n 84 ILE cc_start: 0.8347 (mt) cc_final: 0.8058 (pt) REVERT: o 47 MET cc_start: 0.8456 (tmm) cc_final: 0.7987 (tmm) REVERT: p 636 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7216 (pt) REVERT: e 63 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7351 (mm) REVERT: a 59 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8723 (mm-30) REVERT: a 62 ASP cc_start: 0.8440 (m-30) cc_final: 0.8000 (m-30) REVERT: a 71 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: a 74 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8613 (pttp) REVERT: a 272 LEU cc_start: 0.9279 (mm) cc_final: 0.9076 (mp) REVERT: a 277 ASP cc_start: 0.8078 (m-30) cc_final: 0.7588 (t0) REVERT: a 291 ARG cc_start: 0.7144 (mmp80) cc_final: 0.6756 (mmp80) REVERT: a 395 THR cc_start: 0.8038 (m) cc_final: 0.7819 (p) REVERT: a 406 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7914 (mtp) REVERT: a 467 CYS cc_start: 0.7078 (t) cc_final: 0.6287 (m) REVERT: a 580 MET cc_start: 0.8156 (tpp) cc_final: 0.7800 (tpp) REVERT: a 665 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7653 (mmm160) REVERT: a 752 LEU cc_start: 0.7933 (mt) cc_final: 0.7623 (mt) REVERT: a 759 MET cc_start: 0.6996 (ptt) cc_final: 0.5733 (tmm) outliers start: 170 outliers final: 140 residues processed: 593 average time/residue: 0.1318 time to fit residues: 127.8114 Evaluate side-chains 612 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 457 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 267 ASN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 352 VAL Chi-restraints excluded: chain c residue 365 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 VAL Chi-restraints excluded: chain c residue 400 VAL Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL 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 155 CYS 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 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 225 ILE Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 56 GLN 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 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 53 MET Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 146 LEU Chi-restraints excluded: chain j residue 21 SER 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 124 GLN Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 70 LEU 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 37 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 ILE Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 112 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 7 ASN Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 195 VAL Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 334 GLN Chi-restraints excluded: chain a residue 357 THR Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 471 SER Chi-restraints excluded: chain a residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 296 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 302 optimal weight: 0.6980 chunk 223 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 HIS ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 56 GLN ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN n 123 GLN o 123 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.162538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.137395 restraints weight = 44160.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140979 restraints weight = 21122.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.143249 restraints weight = 12509.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.144627 restraints weight = 8798.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.145230 restraints weight = 7053.205| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24041 Z= 0.160 Angle : 0.728 16.830 32605 Z= 0.358 Chirality : 0.042 0.437 3837 Planarity : 0.005 0.066 4040 Dihedral : 7.624 104.385 3540 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 6.56 % Allowed : 25.45 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.16), residues: 3030 helix: 1.38 (0.11), residues: 2144 sheet: -0.71 (0.50), residues: 93 loop : -2.15 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG n 119 TYR 0.038 0.002 TYR a 562 PHE 0.028 0.002 PHE b 174 TRP 0.043 0.002 TRP a 757 HIS 0.008 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00350 (24030) covalent geometry : angle 0.71571 (32572) hydrogen bonds : bond 0.05808 ( 1688) hydrogen bonds : angle 4.35919 ( 4935) link_BETA1-4 : bond 0.01012 ( 4) link_BETA1-4 : angle 4.77334 ( 12) link_NAG-ASN : bond 0.00596 ( 7) link_NAG-ASN : angle 3.92959 ( 21) ********************** 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 629 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 467 time to evaluate : 0.682 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: 0.7595 (t70) cc_final: 0.6560 (p0) REVERT: c 449 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6232 (m-80) REVERT: b 68 TRP cc_start: 0.8559 (OUTLIER) cc_final: 0.8014 (t60) REVERT: d 101 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.5777 (t80) REVERT: d 107 MET cc_start: 0.6570 (mtp) cc_final: 0.5618 (mtp) REVERT: d 191 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6283 (t80) REVERT: d 259 ARG cc_start: 0.8168 (mpp80) cc_final: 0.7919 (mpp80) REVERT: d 326 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8088 (mm-40) REVERT: f 25 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6656 (ttt) REVERT: g 10 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: g 17 MET cc_start: 0.6302 (ttp) cc_final: 0.5998 (tpt) REVERT: g 112 ILE cc_start: 0.5370 (OUTLIER) cc_final: 0.5148 (mp) REVERT: g 123 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.5586 (mp10) REVERT: h 110 ILE cc_start: 0.6206 (mt) cc_final: 0.5738 (pt) REVERT: i 54 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6568 (mmmt) REVERT: i 139 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: j 17 MET cc_start: 0.7106 (ttt) cc_final: 0.6854 (ttm) REVERT: j 108 PHE cc_start: 0.5311 (OUTLIER) cc_final: 0.4916 (m-80) REVERT: k 44 MET cc_start: 0.8350 (tmm) cc_final: 0.6937 (ppp) REVERT: k 108 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.6028 (m-80) REVERT: l 17 MET cc_start: 0.6584 (mmp) cc_final: 0.5560 (ptm) REVERT: l 23 MET cc_start: 0.6559 (tpt) cc_final: 0.6192 (tpt) REVERT: l 48 ARG cc_start: 0.7119 (mmm160) cc_final: 0.6890 (mmm160) REVERT: l 124 GLN cc_start: 0.7478 (tp-100) cc_final: 0.6680 (tm-30) REVERT: m 48 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8096 (mtm-85) REVERT: n 23 MET cc_start: 0.8276 (tpp) cc_final: 0.8015 (tpt) REVERT: n 84 ILE cc_start: 0.8339 (mt) cc_final: 0.8063 (pt) REVERT: o 47 MET cc_start: 0.8456 (tmm) cc_final: 0.7972 (tmm) REVERT: p 636 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7263 (pt) REVERT: e 63 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7339 (mm) REVERT: a 62 ASP cc_start: 0.8446 (m-30) cc_final: 0.7965 (m-30) REVERT: a 74 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8632 (pttp) REVERT: a 272 LEU cc_start: 0.9267 (mm) cc_final: 0.9066 (mp) REVERT: a 277 ASP cc_start: 0.8105 (m-30) cc_final: 0.7595 (t0) REVERT: a 284 GLN cc_start: 0.8181 (mt0) cc_final: 0.7772 (mt0) REVERT: a 291 ARG cc_start: 0.7234 (mmp80) cc_final: 0.6855 (mmp80) REVERT: a 338 ARG cc_start: 0.8541 (mmt180) cc_final: 0.8322 (mmm-85) REVERT: a 395 THR cc_start: 0.8029 (m) cc_final: 0.7822 (p) REVERT: a 406 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7924 (mtp) REVERT: a 467 CYS cc_start: 0.7073 (t) cc_final: 0.6317 (m) REVERT: a 580 MET cc_start: 0.8163 (tpp) cc_final: 0.7815 (tpp) REVERT: a 651 MET cc_start: 0.7308 (ptp) cc_final: 0.7094 (ptp) REVERT: a 752 LEU cc_start: 0.7898 (mt) cc_final: 0.7614 (mt) REVERT: a 759 MET cc_start: 0.6934 (ptt) cc_final: 0.5755 (tmm) outliers start: 162 outliers final: 138 residues processed: 581 average time/residue: 0.1337 time to fit residues: 127.3965 Evaluate side-chains 612 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 460 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 434 THR Chi-restraints excluded: chain c residue 449 PHE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 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 150 LEU Chi-restraints excluded: chain b residue 155 CYS Chi-restraints excluded: chain b residue 173 LEU 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 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 301 VAL Chi-restraints excluded: chain d residue 308 PHE Chi-restraints excluded: chain d residue 350 ILE Chi-restraints excluded: chain f residue 25 MET Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 40 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 56 GLN 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 123 GLN Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 53 MET Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 128 PHE Chi-restraints excluded: chain h residue 152 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 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 j residue 21 SER 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 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 70 LEU 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 46 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL 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 141 LEU Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 108 PHE Chi-restraints excluded: chain n residue 123 GLN Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 7 ASN Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain o residue 150 LEU Chi-restraints excluded: chain p residue 603 VAL Chi-restraints excluded: chain p residue 617 LEU Chi-restraints excluded: chain p residue 636 ILE Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 73 ILE 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 390 ASN Chi-restraints excluded: chain a residue 406 MET Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 455 LEU Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 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 648 VAL Chi-restraints excluded: chain a residue 658 ILE Chi-restraints excluded: chain a residue 730 LEU Chi-restraints excluded: chain a residue 745 LEU Chi-restraints excluded: chain a residue 763 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 192 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 260 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 0.0970 chunk 88 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN o 123 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 ASN ** 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 = 0.4150 r_free = 0.4150 target = 0.162625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.137506 restraints weight = 44052.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141110 restraints weight = 21009.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.143393 restraints weight = 12408.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.144694 restraints weight = 8717.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145581 restraints weight = 7043.462| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.273 24041 Z= 0.248 Angle : 0.911 59.199 32605 Z= 0.495 Chirality : 0.043 0.435 3837 Planarity : 0.005 0.163 4040 Dihedral : 7.596 104.379 3539 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.51 % Rotamer: Outliers : 6.24 % Allowed : 25.97 % Favored : 67.79 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 3030 helix: 1.39 (0.11), residues: 2144 sheet: -0.70 (0.50), residues: 93 loop : -2.15 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG n 119 TYR 0.029 0.001 TYR a 562 PHE 0.026 0.002 PHE b 174 TRP 0.039 0.002 TRP a 757 HIS 0.007 0.001 HIS a 766 Details of bonding type rmsd covalent geometry : bond 0.00526 (24030) covalent geometry : angle 0.90063 (32572) hydrogen bonds : bond 0.05810 ( 1688) hydrogen bonds : angle 4.37419 ( 4935) link_BETA1-4 : bond 0.01170 ( 4) link_BETA1-4 : angle 4.94946 ( 12) link_NAG-ASN : bond 0.00603 ( 7) link_NAG-ASN : angle 3.92723 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4063.57 seconds wall clock time: 70 minutes 52.46 seconds (4252.46 seconds total)