Starting phenix.real_space_refine on Tue Sep 15 00:54:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tr9_26083/09_2026/7tr9_26083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr9_26083/09_2026/7tr9_26083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tr9_26083/09_2026/7tr9_26083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr9_26083/09_2026/7tr9_26083.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tr9_26083/09_2026/7tr9_26083.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tr9_26083/09_2026/7tr9_26083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tr9_26083/09_2026/7tr9_26083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr9_26083/09_2026/7tr9_26083.map" } resolution = 3.9 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= -0.001 sd= 0.036 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: 6 Type Number sf(0) Gaussians Ni 2 6.56 5 P 74 5.49 5 S 80 5.16 5 C 21635 2.51 5 N 5863 2.21 5 O 6554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34208 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2494 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2134 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "R" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 949 Classifications: {'RNAv2': 45} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 20, 'rna3p': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4307 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1823 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain: "S" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 464 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.19, per 1000 atoms: 0.21 Number of scatterers: 34208 At special positions: 0 Unit cell: (121.52, 150.04, 204.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 S 80 16.00 P 74 15.00 O 6554 8.00 N 5863 7.00 C 21635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 65 " distance=2.03 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 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7808 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 43 sheets defined 36.2% alpha, 10.2% beta 11 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 22 through 29 removed outlier: 3.929A pdb=" N ARG C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 72 removed outlier: 3.843A pdb=" N ARG C 55 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS C 56 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 110 removed outlier: 4.182A pdb=" N ASP C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.630A pdb=" N ALA C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP C 161 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 166 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.533A pdb=" N SER C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 215 through 219 removed outlier: 4.040A pdb=" N LEU C 218 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 removed outlier: 4.264A pdb=" N LEU C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.547A pdb=" N THR C 239 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 278 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.947A pdb=" N ILE C 286 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 287 " --> pdb=" O TYR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 306 removed outlier: 3.527A pdb=" N LEU C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.581A pdb=" N ALA C 318 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 342 removed outlier: 3.565A pdb=" N GLU C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 13 removed outlier: 4.194A pdb=" N ARG D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.541A pdb=" N VAL D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.943A pdb=" N LEU D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 removed outlier: 4.041A pdb=" N GLU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 100 removed outlier: 3.734A pdb=" N ARG D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER D 96 " --> pdb=" O LYS D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.903A pdb=" N ASN E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 removed outlier: 4.322A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.764A pdb=" N LEU E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU E 41 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 removed outlier: 3.742A pdb=" N LYS E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.551A pdb=" N SER E 60 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.800A pdb=" N ILE E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 75 " --> pdb=" O PRO E 71 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.920A pdb=" N LEU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 removed outlier: 4.339A pdb=" N TYR F 11 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 33 removed outlier: 3.667A pdb=" N GLY F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA F 32 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 40 removed outlier: 3.768A pdb=" N LEU F 40 " --> pdb=" O GLN F 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 41 through 49 removed outlier: 3.636A pdb=" N ARG F 49 " --> pdb=" O TYR F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 62 removed outlier: 3.615A pdb=" N LYS F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 76 removed outlier: 4.484A pdb=" N ILE F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 86 through 97 removed outlier: 3.706A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 12 removed outlier: 3.653A pdb=" N TYR G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 33 removed outlier: 3.720A pdb=" N GLY G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 50 removed outlier: 4.210A pdb=" N LEU G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 62 removed outlier: 3.920A pdb=" N LYS G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.596A pdb=" N LEU G 77 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU G 82 " --> pdb=" O GLU G 78 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 94 removed outlier: 4.036A pdb=" N LYS G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.604A pdb=" N ALA G 98 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU G 99 " --> pdb=" O SER G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 99' Processing helix chain 'H' and resid 4 through 14 removed outlier: 4.246A pdb=" N ILE H 8 " --> pdb=" O TRP H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 30 removed outlier: 4.099A pdb=" N GLY H 30 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 4.315A pdb=" N LEU H 40 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU H 42 " --> pdb=" O GLU H 38 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS H 46 " --> pdb=" O GLU H 42 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA H 47 " --> pdb=" O GLY H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 56 Processing helix chain 'H' and resid 57 through 62 removed outlier: 3.553A pdb=" N LYS H 61 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.993A pdb=" N LEU H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 52 through 68 removed outlier: 3.596A pdb=" N VAL I 64 " --> pdb=" O PHE I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.782A pdb=" N LEU I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 82' Processing helix chain 'I' and resid 108 through 113 removed outlier: 3.805A pdb=" N LYS I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 removed outlier: 3.591A pdb=" N VAL I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS I 121 " --> pdb=" O ASP I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 116 through 121' Processing helix chain 'I' and resid 144 through 152 removed outlier: 3.685A pdb=" N ILE I 148 " --> pdb=" O THR I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 240 Processing helix chain 'I' and resid 241 through 243 No H-bonds generated for 'chain 'I' and resid 241 through 243' Processing helix chain 'I' and resid 287 through 299 removed outlier: 4.020A pdb=" N LYS I 295 " --> pdb=" O ARG I 291 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA I 299 " --> pdb=" O LYS I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 333 removed outlier: 3.673A pdb=" N LEU I 328 " --> pdb=" O SER I 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.647A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 Processing helix chain 'J' and resid 108 through 114 removed outlier: 3.606A pdb=" N ILE J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 122 Processing helix chain 'J' and resid 144 through 151 removed outlier: 3.571A pdb=" N ILE J 148 " --> pdb=" O THR J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 180 removed outlier: 3.922A pdb=" N GLY J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR J 180 " --> pdb=" O SER J 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 175 through 180' Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 242 through 247 removed outlier: 3.799A pdb=" N LEU J 246 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 285 No H-bonds generated for 'chain 'J' and resid 283 through 285' Processing helix chain 'J' and resid 286 through 294 removed outlier: 3.527A pdb=" N SER J 292 " --> pdb=" O GLU J 288 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE J 294 " --> pdb=" O ASN J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 Processing helix chain 'J' and resid 324 through 334 Processing helix chain 'K' and resid 51 through 68 removed outlier: 3.944A pdb=" N LEU K 55 " --> pdb=" O THR K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 115 through 122 removed outlier: 3.621A pdb=" N VAL K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 227 through 242 removed outlier: 3.763A pdb=" N LEU K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 3.921A pdb=" N ALA K 289 " --> pdb=" O ASP K 285 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA K 297 " --> pdb=" O ILE K 293 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG K 298 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA K 299 " --> pdb=" O LYS K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 335 removed outlier: 3.950A pdb=" N VAL K 329 " --> pdb=" O VAL K 325 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET K 335 " --> pdb=" O ASN K 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 69 removed outlier: 3.809A pdb=" N THR L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.863A pdb=" N ARG L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 116 through 122 removed outlier: 3.900A pdb=" N VAL L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 152 removed outlier: 3.768A pdb=" N GLU L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 179 removed outlier: 3.592A pdb=" N GLU L 178 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 285 through 299 removed outlier: 3.652A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 335 Processing helix chain 'M' and resid 51 through 66 removed outlier: 4.012A pdb=" N LEU M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 Processing helix chain 'M' and resid 107 through 115 removed outlier: 3.700A pdb=" N LYS M 113 " --> pdb=" O ALA M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 120 removed outlier: 4.003A pdb=" N VAL M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 150 Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 247 Processing helix chain 'M' and resid 285 through 296 removed outlier: 4.168A pdb=" N ALA M 289 " --> pdb=" O ASP M 285 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 333 Processing helix chain 'N' and resid 51 through 68 removed outlier: 3.685A pdb=" N LEU N 55 " --> pdb=" O THR N 51 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 Processing helix chain 'N' and resid 107 through 115 removed outlier: 3.505A pdb=" N ILE N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 150 removed outlier: 3.911A pdb=" N GLU N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 241 removed outlier: 3.582A pdb=" N SER N 237 " --> pdb=" O ALA N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 removed outlier: 4.413A pdb=" N MET N 245 " --> pdb=" O ALA N 241 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 296 removed outlier: 3.695A pdb=" N ILE N 294 " --> pdb=" O ASN N 290 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 301 removed outlier: 3.556A pdb=" N GLY N 301 " --> pdb=" O ARG N 298 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.802A pdb=" N VAL N 333 " --> pdb=" O VAL N 329 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS N 334 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET N 335 " --> pdb=" O ASN N 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 70 removed outlier: 4.478A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS O 56 " --> pdb=" O GLY O 52 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR O 70 " --> pdb=" O TYR O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 removed outlier: 3.530A pdb=" N ARG O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 113 removed outlier: 4.360A pdb=" N LYS O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 121 removed outlier: 3.927A pdb=" N VAL O 120 " --> pdb=" O ALA O 116 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS O 121 " --> pdb=" O ASP O 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 116 through 121' Processing helix chain 'O' and resid 144 through 152 removed outlier: 3.635A pdb=" N GLU O 150 " --> pdb=" O ASP O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 242 through 247 Processing helix chain 'O' and resid 286 through 299 Processing helix chain 'O' and resid 324 through 334 Processing helix chain 'P' and resid 30 through 46 removed outlier: 3.536A pdb=" N GLY P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU P 42 " --> pdb=" O LEU P 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU P 45 " --> pdb=" O GLY P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 69 Processing helix chain 'P' and resid 129 through 141 removed outlier: 3.535A pdb=" N ASN P 134 " --> pdb=" O GLN P 130 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 51 through 59 removed outlier: 4.437A pdb=" N PHE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 95 Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.332A pdb=" N GLU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.791A pdb=" N TYR A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.701A pdb=" N ALA A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.558A pdb=" N LEU A 181 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 240 through 246 removed outlier: 3.674A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 removed outlier: 3.644A pdb=" N GLU A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.598A pdb=" N GLU A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA A 307 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A 309 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.747A pdb=" N GLN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.779A pdb=" N ALA A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.816A pdb=" N ASN A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 399' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.947A pdb=" N LEU A 480 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.563A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'Q' and resid 10 through 23 removed outlier: 3.521A pdb=" N GLU Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 38 removed outlier: 3.751A pdb=" N ILE Q 30 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) Proline residue: Q 31 - end of helix removed outlier: 3.967A pdb=" N ARG Q 35 " --> pdb=" O PRO Q 31 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL Q 36 " --> pdb=" O SER Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 59 Processing helix chain 'Q' and resid 61 through 65 removed outlier: 3.822A pdb=" N CYS Q 65 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 73 Processing helix chain 'Q' and resid 85 through 100 removed outlier: 3.571A pdb=" N ALA Q 89 " --> pdb=" O GLU Q 85 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR Q 90 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN Q 94 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE Q 95 " --> pdb=" O TYR Q 91 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU Q 96 " --> pdb=" O ALA Q 92 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET Q 99 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 113 removed outlier: 4.311A pdb=" N ILE Q 108 " --> pdb=" O THR Q 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY Q 109 " --> pdb=" O ILE Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 143 removed outlier: 3.729A pdb=" N ASP Q 140 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS Q 141 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 156 removed outlier: 4.064A pdb=" N SER Q 154 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE Q 155 " --> pdb=" O GLY Q 151 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE Q 156 " --> pdb=" O THR Q 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 150 through 156' Processing helix chain 'Q' and resid 156 through 161 removed outlier: 4.153A pdb=" N ILE Q 160 " --> pdb=" O ILE Q 156 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS Q 161 " --> pdb=" O LYS Q 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 156 through 161' Processing helix chain 'Q' and resid 178 through 191 removed outlier: 3.650A pdb=" N ARG Q 184 " --> pdb=" O ARG Q 180 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER Q 186 " --> pdb=" O VAL Q 182 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS Q 191 " --> pdb=" O VAL Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 210 removed outlier: 4.745A pdb=" N VAL Q 202 " --> pdb=" O LEU Q 198 " (cutoff:3.500A) Proline residue: Q 208 - end of helix Processing helix chain 'Q' and resid 211 through 216 removed outlier: 4.128A pdb=" N GLY Q 215 " --> pdb=" O CYS Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 231 removed outlier: 3.647A pdb=" N ALA Q 227 " --> pdb=" O ALA Q 224 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA Q 228 " --> pdb=" O ALA Q 225 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA Q 229 " --> pdb=" O ALA Q 226 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA Q 231 " --> pdb=" O ALA Q 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 37 Processing sheet with id=AA2, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA3, first strand: chain 'C' and resid 170 through 173 removed outlier: 3.531A pdb=" N ILE C 181 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 136 through 137 removed outlier: 3.505A pdb=" N LYS I 137 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 199 " --> pdb=" O LYS I 137 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL I 3 " --> pdb=" O LEU I 200 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU I 265 " --> pdb=" O ARG I 8 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG I 10 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL I 263 " --> pdb=" O ARG I 10 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL I 306 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL I 322 " --> pdb=" O VAL I 306 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR I 308 " --> pdb=" O VAL I 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 26 through 27 removed outlier: 3.781A pdb=" N GLU I 188 " --> pdb=" O ILE I 27 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 32 through 38 removed outlier: 3.578A pdb=" N VAL I 34 " --> pdb=" O VAL I 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 123 through 125 removed outlier: 4.410A pdb=" N ALA I 125 " --> pdb=" O ARG I 130 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG I 130 " --> pdb=" O ALA I 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 2 through 9 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 2 through 9 current: chain 'J' and resid 194 through 196 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 194 through 196 current: chain 'J' and resid 305 through 309 Processing sheet with id=AA9, first strand: chain 'J' and resid 18 through 19 Processing sheet with id=AB1, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AB2, first strand: chain 'J' and resid 123 through 124 removed outlier: 4.185A pdb=" N PHE J 123 " --> pdb=" O ARG J 132 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG J 132 " --> pdb=" O PHE J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'J' and resid 157 through 163 Processing sheet with id=AB4, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 184 through 200 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 184 through 200 current: chain 'K' and resid 305 through 308 removed outlier: 3.804A pdb=" N THR K 320 " --> pdb=" O VAL K 306 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AB6, first strand: chain 'K' and resid 95 through 96 Processing sheet with id=AB7, first strand: chain 'K' and resid 123 through 125 removed outlier: 3.535A pdb=" N ARG K 132 " --> pdb=" O PHE K 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 186 through 196 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 186 through 196 current: chain 'L' and resid 305 through 309 removed outlier: 6.386A pdb=" N VAL L 306 " --> pdb=" O THR L 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AC1, first strand: chain 'L' and resid 95 through 96 Processing sheet with id=AC2, first strand: chain 'L' and resid 123 through 125 removed outlier: 3.541A pdb=" N ARG L 132 " --> pdb=" O PHE L 123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 2 through 9 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 9 current: chain 'M' and resid 194 through 196 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 194 through 196 current: chain 'M' and resid 306 through 309 removed outlier: 6.990A pdb=" N VAL M 306 " --> pdb=" O THR M 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'M' and resid 26 through 27 Processing sheet with id=AC5, first strand: chain 'M' and resid 32 through 36 Processing sheet with id=AC6, first strand: chain 'M' and resid 95 through 96 Processing sheet with id=AC7, first strand: chain 'M' and resid 123 through 124 removed outlier: 3.813A pdb=" N PHE M 123 " --> pdb=" O ARG M 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG M 132 " --> pdb=" O PHE M 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 213 through 215 Processing sheet with id=AC9, first strand: chain 'N' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 3 through 14 current: chain 'N' and resid 184 through 200 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 184 through 200 current: chain 'N' and resid 305 through 309 Processing sheet with id=AD1, first strand: chain 'N' and resid 34 through 36 Processing sheet with id=AD2, first strand: chain 'N' and resid 95 through 96 Processing sheet with id=AD3, first strand: chain 'N' and resid 123 through 125 Processing sheet with id=AD4, first strand: chain 'O' and resid 2 through 10 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 2 through 10 current: chain 'O' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 193 through 201 current: chain 'O' and resid 304 through 309 removed outlier: 8.598A pdb=" N THR O 320 " --> pdb=" O ILE O 304 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL O 306 " --> pdb=" O THR O 320 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL O 322 " --> pdb=" O VAL O 306 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR O 308 " --> pdb=" O VAL O 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'O' and resid 31 through 35 Processing sheet with id=AD6, first strand: chain 'O' and resid 94 through 96 Processing sheet with id=AD7, first strand: chain 'O' and resid 123 through 125 removed outlier: 4.191A pdb=" N PHE O 123 " --> pdb=" O ARG O 132 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG O 132 " --> pdb=" O PHE O 123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 76 through 80 removed outlier: 3.507A pdb=" N SER P 77 " --> pdb=" O ALA P 122 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU P 119 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP P 157 " --> pdb=" O CYS P 7 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 85 through 86 Processing sheet with id=AE1, first strand: chain 'P' and resid 91 through 94 removed outlier: 4.379A pdb=" N ASP P 107 " --> pdb=" O ARG P 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 168 through 169 removed outlier: 4.531A pdb=" N ALA P 168 " --> pdb=" O VAL P 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL P 240 " --> pdb=" O ALA P 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'P' and resid 174 through 175 removed outlier: 3.733A pdb=" N PHE P 217 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU P 198 " --> pdb=" O PHE P 217 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 243 through 246 removed outlier: 3.575A pdb=" N VAL P 246 " --> pdb=" O GLU P 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.636A pdb=" N ILE A 197 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 199 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 196 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 164 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 198 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 69 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 131 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR A 71 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.700A pdb=" N ARG A 144 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 232 through 238 removed outlier: 6.176A pdb=" N LYS A 233 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE A 361 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG A 235 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ILE A 363 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A 237 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL A 332 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A 362 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N THR A 334 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 259 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 258 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA A 316 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL A 260 " --> pdb=" O ALA A 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 835 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 6.59 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8612 1.33 - 1.45: 6704 1.45 - 1.57: 19418 1.57 - 1.70: 147 1.70 - 1.82: 144 Bond restraints: 35025 Sorted by residual: bond pdb=" O3' DT S 46 " pdb=" P DG S 47 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.20e-02 6.94e+03 3.64e+01 bond pdb=" CA SER L 134 " pdb=" CB SER L 134 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.35e-02 5.49e+03 2.06e+01 bond pdb=" C6 DG S 49 " pdb=" O6 DG S 49 " ideal model delta sigma weight residual 1.237 1.277 -0.040 9.00e-03 1.23e+04 1.98e+01 bond pdb=" O3' DG S 47 " pdb=" P DG S 48 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.20e-02 6.94e+03 1.83e+01 bond pdb=" N GLY J 21 " pdb=" CA GLY J 21 " ideal model delta sigma weight residual 1.446 1.481 -0.035 9.50e-03 1.11e+04 1.33e+01 ... (remaining 35020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 46776 2.28 - 4.57: 892 4.57 - 6.85: 125 6.85 - 9.14: 11 9.14 - 11.42: 5 Bond angle restraints: 47809 Sorted by residual: angle pdb=" C ASN I 163 " pdb=" N ARG I 164 " pdb=" CA ARG I 164 " ideal model delta sigma weight residual 123.14 112.98 10.16 1.48e+00 4.57e-01 4.71e+01 angle pdb=" C THR J 51 " pdb=" CA THR J 51 " pdb=" CB THR J 51 " ideal model delta sigma weight residual 109.46 98.04 11.42 1.84e+00 2.95e-01 3.85e+01 angle pdb=" N ASN K 53 " pdb=" CA ASN K 53 " pdb=" C ASN K 53 " ideal model delta sigma weight residual 111.28 104.59 6.69 1.09e+00 8.42e-01 3.76e+01 angle pdb=" N ASN J 53 " pdb=" CA ASN J 53 " pdb=" C ASN J 53 " ideal model delta sigma weight residual 111.07 104.51 6.56 1.07e+00 8.73e-01 3.75e+01 angle pdb=" N VAL O 74 " pdb=" CA VAL O 74 " pdb=" C VAL O 74 " ideal model delta sigma weight residual 113.71 108.02 5.69 9.50e-01 1.11e+00 3.59e+01 ... (remaining 47804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 20546 35.63 - 71.27: 406 71.27 - 106.90: 21 106.90 - 142.54: 0 142.54 - 178.17: 2 Dihedral angle restraints: 20975 sinusoidal: 8838 harmonic: 12137 Sorted by residual: dihedral pdb=" C4' G R 8 " pdb=" C3' G R 8 " pdb=" C2' G R 8 " pdb=" C1' G R 8 " ideal model delta sinusoidal sigma weight residual 36.34 -36.19 72.54 1 3.10e+00 1.04e-01 6.99e+02 dihedral pdb=" C4' G R 42 " pdb=" C3' G R 42 " pdb=" C2' G R 42 " pdb=" C1' G R 42 " ideal model delta sinusoidal sigma weight residual 36.34 -35.93 72.28 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' U R 44 " pdb=" C3' U R 44 " pdb=" C2' U R 44 " pdb=" C1' U R 44 " ideal model delta sinusoidal sigma weight residual 36.34 -35.92 72.26 1 3.10e+00 1.04e-01 6.95e+02 ... (remaining 20972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 5047 0.089 - 0.178: 367 0.178 - 0.268: 66 0.268 - 0.357: 22 0.357 - 0.446: 3 Chirality restraints: 5505 Sorted by residual: chirality pdb=" P G R 12 " pdb=" OP1 G R 12 " pdb=" OP2 G R 12 " pdb=" O5' G R 12 " both_signs ideal model delta sigma weight residual True 2.17 -2.62 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" P G R 10 " pdb=" OP1 G R 10 " pdb=" OP2 G R 10 " pdb=" O5' G R 10 " both_signs ideal model delta sigma weight residual True 2.17 -2.61 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA ASN J 53 " pdb=" N ASN J 53 " pdb=" C ASN J 53 " pdb=" CB ASN J 53 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 5502 not shown) Planarity restraints: 5856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT S 46 " 0.058 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" N1 DT S 46 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DT S 46 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT S 46 " -0.040 2.00e-02 2.50e+03 pdb=" N3 DT S 46 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT S 46 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT S 46 " 0.053 2.00e-02 2.50e+03 pdb=" C5 DT S 46 " -0.006 2.00e-02 2.50e+03 pdb=" C7 DT S 46 " -0.035 2.00e-02 2.50e+03 pdb=" C6 DT S 46 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 181 " -0.024 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ALA J 181 " 0.079 2.00e-02 2.50e+03 pdb=" O ALA J 181 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN J 182 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 130 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ARG L 130 " -0.078 2.00e-02 2.50e+03 pdb=" O ARG L 130 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG L 131 " 0.026 2.00e-02 2.50e+03 ... (remaining 5853 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.79: 8501 2.79 - 3.49: 50398 3.49 - 4.20: 86084 4.20 - 4.90: 144475 Nonbonded interactions: 289461 Sorted by model distance: nonbonded pdb="NI NI Q 301 " pdb="NI NI Q 302 " model vdw 1.387 1.320 nonbonded pdb=" NZ LYS C 136 " pdb=" N7 DG S 61 " model vdw 1.635 3.200 nonbonded pdb=" OD2 ASP Q 61 " pdb="NI NI Q 301 " model vdw 2.039 2.180 nonbonded pdb=" OD2 ASP Q 61 " pdb="NI NI Q 302 " model vdw 2.090 2.180 nonbonded pdb=" NH1 ARG P 95 " pdb=" OP1 DG S 60 " model vdw 2.117 3.120 ... (remaining 289456 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 'D' selection = (chain 'E' and resid 3 through 109) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 164 or resid 180 th \ rough 335)) selection = (chain 'J' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 164 or resid 180 through 335)) selection = (chain 'K' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'L' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'M' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'N' and resid 1 through 335) } 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: 2.530 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: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.330 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 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: 39.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 : 0.003 0.083 35031 Z= 0.187 Angle : 0.705 11.423 47821 Z= 0.389 Chirality : 0.056 0.446 5505 Planarity : 0.004 0.047 5856 Dihedral : 13.553 178.172 13149 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.74 % Favored : 90.88 % Rotamer: Outliers : 0.17 % Allowed : 0.79 % Favored : 99.04 % Cbeta Deviations : 0.05 % 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 are not related in a simple way. whole: -2.44 (0.13), residues: 4144 helix: -0.87 (0.16), residues: 1193 sheet: -0.76 (0.22), residues: 544 loop : -2.32 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 132 TYR 0.032 0.001 TYR P 20 PHE 0.020 0.001 PHE J 60 TRP 0.026 0.001 TRP G 4 HIS 0.007 0.001 HIS I 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.19 (35025) covalent geometry : angle 0.70461 / 0.39 (47809) SS BOND : bond 0.00027 / 0.01 ( 6) SS BOND : angle 0.20403 / 0.12 ( 12) hydrogen bonds : bond 0.19597 / 13.29 ( 864) hydrogen bonds : angle 7.11850 / 5.03 ( 2380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 885 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 ASP cc_start: 0.8641 (p0) cc_final: 0.7569 (t70) REVERT: C 220 ASN cc_start: 0.7728 (t0) cc_final: 0.7522 (t0) REVERT: C 222 ARG cc_start: 0.8531 (ttm110) cc_final: 0.7690 (mtm110) REVERT: C 263 GLU cc_start: 0.7362 (pt0) cc_final: 0.6771 (pt0) REVERT: C 276 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8334 (ttmt) REVERT: C 298 GLU cc_start: 0.8625 (pm20) cc_final: 0.8422 (pm20) REVERT: D 35 ARG cc_start: 0.6833 (ptp90) cc_final: 0.5942 (mtt90) REVERT: D 95 VAL cc_start: 0.9186 (p) cc_final: 0.8393 (p) REVERT: E 59 GLU cc_start: 0.7956 (pt0) cc_final: 0.7725 (pm20) REVERT: F 33 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7335 (pttm) REVERT: F 78 GLU cc_start: 0.8502 (mp0) cc_final: 0.8114 (mp0) REVERT: F 99 LEU cc_start: 0.8999 (mt) cc_final: 0.8693 (mt) REVERT: G 29 ASP cc_start: 0.8107 (m-30) cc_final: 0.7876 (m-30) REVERT: G 42 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8687 (tm-30) REVERT: G 72 GLU cc_start: 0.8327 (pm20) cc_final: 0.8007 (pm20) REVERT: I 123 PHE cc_start: 0.8269 (p90) cc_final: 0.8037 (p90) REVERT: I 148 ILE cc_start: 0.7907 (mm) cc_final: 0.7654 (mm) REVERT: I 306 VAL cc_start: 0.8813 (t) cc_final: 0.8427 (p) REVERT: J 27 ILE cc_start: 0.7850 (mm) cc_final: 0.7426 (mm) REVERT: J 54 MET cc_start: 0.8246 (ttt) cc_final: 0.7652 (tpp) REVERT: J 60 PHE cc_start: 0.8834 (t80) cc_final: 0.8621 (t80) REVERT: J 107 ASP cc_start: 0.7637 (t70) cc_final: 0.7272 (t70) REVERT: J 119 ASP cc_start: 0.7303 (t0) cc_final: 0.7077 (t0) REVERT: J 163 ASN cc_start: 0.8548 (p0) cc_final: 0.8315 (p0) REVERT: J 213 VAL cc_start: 0.7515 (m) cc_final: 0.7220 (m) REVERT: J 227 ASP cc_start: 0.8733 (t70) cc_final: 0.8424 (t0) REVERT: J 245 MET cc_start: 0.9127 (mmp) cc_final: 0.8862 (mmt) REVERT: J 285 ASP cc_start: 0.7682 (p0) cc_final: 0.7467 (p0) REVERT: K 14 HIS cc_start: 0.7865 (p90) cc_final: 0.7525 (p90) REVERT: K 17 ASN cc_start: 0.8189 (t0) cc_final: 0.6883 (t0) REVERT: K 183 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5778 (tpp) REVERT: L 27 ILE cc_start: 0.8402 (mm) cc_final: 0.8191 (tp) REVERT: L 39 GLU cc_start: 0.8787 (pt0) cc_final: 0.8578 (pp20) REVERT: L 63 PHE cc_start: 0.7005 (t80) cc_final: 0.6597 (t80) REVERT: L 166 ASP cc_start: 0.5868 (t0) cc_final: 0.5512 (p0) REVERT: L 254 LEU cc_start: 0.8824 (mm) cc_final: 0.8557 (mt) REVERT: L 283 TYR cc_start: 0.6421 (m-80) cc_final: 0.6130 (m-80) REVERT: M 9 ILE cc_start: 0.7789 (pt) cc_final: 0.7513 (pt) REVERT: M 11 LEU cc_start: 0.8884 (tp) cc_final: 0.8604 (tp) REVERT: M 19 GLN cc_start: 0.7980 (mp10) cc_final: 0.7512 (mp10) REVERT: M 28 GLU cc_start: 0.8382 (pp20) cc_final: 0.7703 (pp20) REVERT: M 63 PHE cc_start: 0.7923 (t80) cc_final: 0.7313 (t80) REVERT: M 123 PHE cc_start: 0.8255 (p90) cc_final: 0.7874 (p90) REVERT: M 135 LEU cc_start: 0.7050 (mp) cc_final: 0.6622 (mp) REVERT: M 207 ILE cc_start: 0.7091 (mt) cc_final: 0.6829 (mt) REVERT: M 211 LEU cc_start: 0.8746 (mt) cc_final: 0.8470 (tt) REVERT: M 229 ASN cc_start: 0.8104 (t0) cc_final: 0.7643 (t0) REVERT: M 250 ILE cc_start: 0.8535 (mp) cc_final: 0.8234 (mp) REVERT: M 261 PHE cc_start: 0.8366 (t80) cc_final: 0.7573 (t80) REVERT: N 2 TYR cc_start: 0.7305 (m-80) cc_final: 0.7102 (m-10) REVERT: N 27 ILE cc_start: 0.8563 (mp) cc_final: 0.8150 (pt) REVERT: N 59 HIS cc_start: 0.9312 (t-90) cc_final: 0.8625 (t-90) REVERT: N 60 PHE cc_start: 0.8208 (t80) cc_final: 0.7633 (t80) REVERT: N 65 ASP cc_start: 0.9068 (m-30) cc_final: 0.8808 (m-30) REVERT: N 147 PHE cc_start: 0.8263 (t80) cc_final: 0.8005 (t80) REVERT: N 160 ILE cc_start: 0.8697 (pt) cc_final: 0.8398 (pt) REVERT: N 162 HIS cc_start: 0.5767 (m170) cc_final: 0.4813 (m170) REVERT: N 187 ARG cc_start: 0.5244 (mpp-170) cc_final: 0.4869 (mpp-170) REVERT: N 282 PHE cc_start: 0.8530 (t80) cc_final: 0.8132 (t80) REVERT: N 333 VAL cc_start: 0.8337 (t) cc_final: 0.7898 (t) REVERT: N 334 LYS cc_start: 0.8162 (pttt) cc_final: 0.7816 (mmtt) REVERT: O 110 THR cc_start: 0.9004 (p) cc_final: 0.8596 (p) REVERT: O 194 TYR cc_start: 0.6994 (m-80) cc_final: 0.6508 (m-80) REVERT: O 279 VAL cc_start: 0.9559 (m) cc_final: 0.9346 (p) REVERT: P 13 PHE cc_start: 0.6711 (m-80) cc_final: 0.6422 (m-80) REVERT: P 115 PHE cc_start: 0.7230 (t80) cc_final: 0.6967 (t80) REVERT: P 172 PHE cc_start: 0.8041 (m-80) cc_final: 0.7463 (m-80) REVERT: P 200 MET cc_start: 0.6908 (tpt) cc_final: 0.6472 (tpp) REVERT: A 41 VAL cc_start: 0.7945 (p) cc_final: 0.7729 (p) REVERT: A 52 VAL cc_start: 0.8354 (p) cc_final: 0.7907 (m) REVERT: A 107 LEU cc_start: 0.9248 (tp) cc_final: 0.9013 (pp) REVERT: A 118 LEU cc_start: 0.8480 (tp) cc_final: 0.8112 (tp) REVERT: A 198 MET cc_start: 0.8603 (ptp) cc_final: 0.7743 (tpp) REVERT: A 246 ASN cc_start: 0.8620 (m110) cc_final: 0.8353 (p0) REVERT: A 264 THR cc_start: 0.7761 (m) cc_final: 0.7453 (m) REVERT: A 441 TYR cc_start: 0.6894 (p90) cc_final: 0.6675 (p90) REVERT: Q 28 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8567 (mmmt) REVERT: Q 115 MET cc_start: 0.8876 (mmp) cc_final: 0.8467 (mmm) REVERT: Q 159 MET cc_start: 0.5490 (pmm) cc_final: 0.5237 (pmm) REVERT: Q 213 TYR cc_start: 0.7139 (t80) cc_final: 0.6798 (t80) outliers start: 6 outliers final: 1 residues processed: 889 average time/residue: 0.2237 time to fit residues: 317.0345 Evaluate side-chains 532 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 530 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain K residue 183 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN E 7 ASN ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 310 ASN J 53 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN J 104 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 59 HIS ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 GLN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.098618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.084190 restraints weight = 164801.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.086510 restraints weight = 101327.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.088118 restraints weight = 69808.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.089244 restraints weight = 52128.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.090056 restraints weight = 41506.698| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 35031 Z= 0.237 Angle : 0.940 30.930 47821 Z= 0.438 Chirality : 0.075 1.335 5505 Planarity : 0.006 0.098 5856 Dihedral : 11.676 169.812 5404 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.86 % Favored : 90.78 % Rotamer: Outliers : 2.30 % Allowed : 13.41 % Favored : 84.29 % 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 are not related in a simple way. whole: -2.54 (0.12), residues: 4144 helix: -0.96 (0.14), residues: 1276 sheet: -0.81 (0.22), residues: 571 loop : -2.42 (0.12), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 180 TYR 0.028 0.002 TYR F 14 PHE 0.038 0.003 PHE I 282 TRP 0.021 0.002 TRP D 4 HIS 0.013 0.002 HIS L 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (35025) covalent geometry : angle 0.93940 / 0.44 (47809) SS BOND : bond 0.03289 / 1.64 ( 6) SS BOND : angle 1.54195 / 0.95 ( 12) hydrogen bonds : bond 0.04986 / 3.30 ( 864) hydrogen bonds : angle 5.45453 / 3.80 ( 2380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 559 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 HIS cc_start: 0.8905 (m-70) cc_final: 0.8291 (m90) REVERT: C 60 ASP cc_start: 0.8888 (m-30) cc_final: 0.8667 (m-30) REVERT: C 131 MET cc_start: 0.8636 (tmm) cc_final: 0.8372 (tmm) REVERT: C 177 ASP cc_start: 0.8737 (p0) cc_final: 0.7830 (t70) REVERT: C 205 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.5642 (mtt) REVERT: C 276 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8369 (ttmt) REVERT: C 304 ILE cc_start: 0.9079 (tp) cc_final: 0.8741 (tp) REVERT: D 48 LEU cc_start: 0.8113 (tp) cc_final: 0.7877 (tp) REVERT: F 49 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7642 (mmm160) REVERT: G 29 ASP cc_start: 0.8284 (m-30) cc_final: 0.7713 (m-30) REVERT: G 42 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8629 (tm-30) REVERT: G 72 GLU cc_start: 0.7966 (pm20) cc_final: 0.7695 (pm20) REVERT: H 25 TYR cc_start: 0.7691 (m-10) cc_final: 0.7260 (m-10) REVERT: I 1 MET cc_start: 0.7839 (mmm) cc_final: 0.7393 (mmm) REVERT: I 306 VAL cc_start: 0.8833 (t) cc_final: 0.8590 (p) REVERT: J 107 ASP cc_start: 0.7314 (t70) cc_final: 0.7069 (t70) REVERT: J 119 ASP cc_start: 0.7353 (t0) cc_final: 0.6801 (t0) REVERT: J 184 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7371 (tp) REVERT: J 213 VAL cc_start: 0.7704 (m) cc_final: 0.7469 (m) REVERT: J 232 LYS cc_start: 0.8389 (tttt) cc_final: 0.7696 (tptt) REVERT: J 285 ASP cc_start: 0.7282 (p0) cc_final: 0.6952 (p0) REVERT: K 17 ASN cc_start: 0.7469 (t0) cc_final: 0.6882 (t0) REVERT: L 63 PHE cc_start: 0.7221 (t80) cc_final: 0.6835 (t80) REVERT: L 166 ASP cc_start: 0.5929 (t0) cc_final: 0.5671 (p0) REVERT: L 207 ILE cc_start: 0.7626 (mm) cc_final: 0.7391 (mm) REVERT: M 19 GLN cc_start: 0.8217 (mp10) cc_final: 0.7468 (mp10) REVERT: M 60 PHE cc_start: 0.6886 (t80) cc_final: 0.6438 (t80) REVERT: M 88 PHE cc_start: 0.6533 (m-80) cc_final: 0.6140 (m-80) REVERT: M 135 LEU cc_start: 0.7380 (mp) cc_final: 0.7064 (mp) REVERT: M 211 LEU cc_start: 0.8791 (mt) cc_final: 0.8549 (tt) REVERT: N 10 ARG cc_start: 0.6658 (mtp180) cc_final: 0.5997 (mtp180) REVERT: N 59 HIS cc_start: 0.9383 (t-90) cc_final: 0.8873 (t-90) REVERT: N 147 PHE cc_start: 0.8364 (t80) cc_final: 0.8140 (t80) REVERT: N 202 LEU cc_start: 0.8165 (tp) cc_final: 0.7940 (tp) REVERT: N 237 SER cc_start: 0.9197 (t) cc_final: 0.8972 (p) REVERT: N 258 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6640 (t80) REVERT: O 194 TYR cc_start: 0.6702 (m-80) cc_final: 0.6302 (m-80) REVERT: P 10 PHE cc_start: 0.8301 (p90) cc_final: 0.8037 (p90) REVERT: P 89 PHE cc_start: 0.7911 (m-10) cc_final: 0.7226 (m-10) REVERT: P 115 PHE cc_start: 0.7708 (t80) cc_final: 0.7474 (t80) REVERT: P 172 PHE cc_start: 0.7819 (m-80) cc_final: 0.7245 (m-80) REVERT: A 107 LEU cc_start: 0.9405 (tp) cc_final: 0.9119 (pp) REVERT: A 118 LEU cc_start: 0.8269 (tp) cc_final: 0.7948 (tp) REVERT: A 177 MET cc_start: 0.6016 (mmt) cc_final: 0.5682 (mmt) REVERT: A 246 ASN cc_start: 0.8511 (m110) cc_final: 0.8177 (p0) REVERT: A 340 ASP cc_start: 0.8737 (t0) cc_final: 0.8224 (m-30) REVERT: Q 27 ASN cc_start: 0.8810 (t0) cc_final: 0.8497 (t0) REVERT: Q 99 MET cc_start: 0.6973 (ppp) cc_final: 0.6490 (ppp) REVERT: Q 115 MET cc_start: 0.8816 (mmp) cc_final: 0.8461 (mmm) REVERT: Q 161 LYS cc_start: 0.8377 (mmtm) cc_final: 0.7829 (tmmt) outliers start: 79 outliers final: 46 residues processed: 603 average time/residue: 0.2103 time to fit residues: 206.7598 Evaluate side-chains 500 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 450 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 183 MET Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 258 PHE Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 310 ASN Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 102 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 382 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 414 optimal weight: 20.0000 chunk 386 optimal weight: 40.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 ASN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 GLN K 223 ASN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 229 ASN ** M 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 GLN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 310 ASN O 90 GLN O 296 ASN ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 328 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.091393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.076662 restraints weight = 164948.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.078890 restraints weight = 99772.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.080424 restraints weight = 68518.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.081484 restraints weight = 51423.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.082230 restraints weight = 41325.772| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 35031 Z= 0.272 Angle : 0.882 13.302 47821 Z= 0.430 Chirality : 0.060 0.733 5505 Planarity : 0.006 0.077 5856 Dihedral : 12.366 171.158 5401 Min Nonbonded Distance : 0.942 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.27 % Favored : 90.44 % Rotamer: Outliers : 3.67 % Allowed : 16.68 % Favored : 79.65 % 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 are not related in a simple way. whole: -2.55 (0.12), residues: 4144 helix: -0.97 (0.14), residues: 1282 sheet: -0.98 (0.21), residues: 615 loop : -2.41 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 87 TYR 0.051 0.003 TYR C 20 PHE 0.032 0.003 PHE L 140 TRP 0.029 0.002 TRP H 105 HIS 0.014 0.002 HIS K 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.27 (35025) covalent geometry : angle 0.88230 / 0.43 (47809) SS BOND : bond 0.01075 / 0.54 ( 6) SS BOND : angle 0.84247 / 0.52 ( 12) hydrogen bonds : bond 0.04838 / 3.28 ( 864) hydrogen bonds : angle 5.37318 / 3.73 ( 2380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 505 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8647 (mm) REVERT: C 60 ASP cc_start: 0.8993 (m-30) cc_final: 0.8696 (m-30) REVERT: C 62 LEU cc_start: 0.8895 (mm) cc_final: 0.8660 (pp) REVERT: C 177 ASP cc_start: 0.8872 (p0) cc_final: 0.7978 (t70) REVERT: C 205 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.5766 (mtt) REVERT: C 312 LEU cc_start: 0.9220 (tp) cc_final: 0.9018 (tp) REVERT: D 38 GLU cc_start: 0.7986 (pt0) cc_final: 0.7750 (mt-10) REVERT: D 48 LEU cc_start: 0.8504 (tp) cc_final: 0.8196 (tp) REVERT: E 46 LYS cc_start: 0.9387 (mmmm) cc_final: 0.9087 (mmmm) REVERT: E 53 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.5654 (mmtp) REVERT: E 88 LYS cc_start: 0.9093 (tptt) cc_final: 0.8831 (tppt) REVERT: E 92 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8664 (pttm) REVERT: F 46 LYS cc_start: 0.9235 (mttp) cc_final: 0.9023 (tptt) REVERT: G 29 ASP cc_start: 0.8045 (m-30) cc_final: 0.7584 (m-30) REVERT: G 42 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8487 (tm-30) REVERT: G 49 ARG cc_start: 0.9464 (mmm160) cc_final: 0.9259 (mmm160) REVERT: G 72 GLU cc_start: 0.8069 (pm20) cc_final: 0.7847 (pm20) REVERT: H 25 TYR cc_start: 0.7708 (m-10) cc_final: 0.7227 (m-10) REVERT: H 33 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8553 (pttm) REVERT: H 41 LEU cc_start: 0.5676 (mt) cc_final: 0.5028 (pp) REVERT: I 1 MET cc_start: 0.7312 (mmm) cc_final: 0.6526 (tpp) REVERT: I 54 MET cc_start: 0.8428 (mmp) cc_final: 0.8141 (mmm) REVERT: I 63 PHE cc_start: 0.8418 (t80) cc_final: 0.8078 (t80) REVERT: I 306 VAL cc_start: 0.9102 (t) cc_final: 0.8783 (p) REVERT: J 107 ASP cc_start: 0.7369 (t70) cc_final: 0.7162 (t70) REVERT: J 119 ASP cc_start: 0.7385 (t0) cc_final: 0.6929 (t0) REVERT: J 184 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7173 (mt) REVERT: J 250 ILE cc_start: 0.9068 (mp) cc_final: 0.8656 (mm) REVERT: J 285 ASP cc_start: 0.7354 (p0) cc_final: 0.7016 (p0) REVERT: K 17 ASN cc_start: 0.7587 (t0) cc_final: 0.6756 (t0) REVERT: L 63 PHE cc_start: 0.7616 (t80) cc_final: 0.7333 (t80) REVERT: L 166 ASP cc_start: 0.6175 (t0) cc_final: 0.5584 (p0) REVERT: L 207 ILE cc_start: 0.8170 (mm) cc_final: 0.7837 (mm) REVERT: L 283 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.4614 (m-80) REVERT: M 9 ILE cc_start: 0.8413 (pt) cc_final: 0.8053 (mm) REVERT: M 60 PHE cc_start: 0.7380 (t80) cc_final: 0.6862 (t80) REVERT: M 135 LEU cc_start: 0.8192 (mp) cc_final: 0.7930 (mp) REVERT: M 261 PHE cc_start: 0.8406 (t80) cc_final: 0.7809 (t80) REVERT: N 59 HIS cc_start: 0.9495 (t-90) cc_final: 0.9170 (t-90) REVERT: N 258 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6900 (t80) REVERT: N 266 LEU cc_start: 0.8447 (mt) cc_final: 0.8158 (mt) REVERT: O 31 LYS cc_start: 0.7854 (mppt) cc_final: 0.7581 (mmtm) REVERT: O 194 TYR cc_start: 0.6818 (m-80) cc_final: 0.6443 (m-80) REVERT: P 10 PHE cc_start: 0.8520 (p90) cc_final: 0.8073 (p90) REVERT: P 12 PHE cc_start: 0.8369 (m-80) cc_final: 0.7705 (m-80) REVERT: P 89 PHE cc_start: 0.8482 (m-10) cc_final: 0.8239 (m-10) REVERT: P 134 ASN cc_start: 0.8435 (p0) cc_final: 0.7961 (p0) REVERT: P 172 PHE cc_start: 0.8297 (m-80) cc_final: 0.7404 (m-80) REVERT: A 60 TYR cc_start: 0.7167 (t80) cc_final: 0.6842 (t80) REVERT: A 107 LEU cc_start: 0.9352 (tp) cc_final: 0.9127 (pp) REVERT: A 118 LEU cc_start: 0.8399 (tp) cc_final: 0.8050 (tp) REVERT: A 140 LEU cc_start: 0.8615 (pp) cc_final: 0.7966 (mt) REVERT: A 177 MET cc_start: 0.6243 (mmt) cc_final: 0.5972 (mmm) REVERT: A 236 LEU cc_start: 0.6207 (mm) cc_final: 0.5953 (tp) REVERT: A 238 GLU cc_start: 0.8079 (tp30) cc_final: 0.7309 (tp30) REVERT: A 246 ASN cc_start: 0.8736 (m110) cc_final: 0.8309 (p0) REVERT: A 301 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7992 (tmm-80) REVERT: Q 37 MET cc_start: 0.8556 (tmm) cc_final: 0.8295 (tmm) REVERT: Q 50 ASP cc_start: 0.8293 (m-30) cc_final: 0.7878 (m-30) REVERT: Q 115 MET cc_start: 0.8742 (mmp) cc_final: 0.8471 (mmm) REVERT: Q 149 MET cc_start: 0.5017 (pmm) cc_final: 0.4677 (pmm) REVERT: Q 159 MET cc_start: 0.5313 (pmm) cc_final: 0.4823 (pmm) REVERT: Q 161 LYS cc_start: 0.8425 (mmtm) cc_final: 0.7917 (tmmt) REVERT: Q 169 LYS cc_start: 0.1115 (OUTLIER) cc_final: -0.0975 (ptmm) outliers start: 126 outliers final: 65 residues processed: 592 average time/residue: 0.2063 time to fit residues: 201.1739 Evaluate side-chains 503 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 428 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 312 ASP Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 227 ASP Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 258 PHE Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 72 TYR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 127 LYS Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 310 ASN Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 169 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 172 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN H 37 GLN I 53 ASN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.089893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.075216 restraints weight = 162836.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.077443 restraints weight = 97027.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.078948 restraints weight = 66001.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.079992 restraints weight = 49382.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.080733 restraints weight = 39554.113| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35031 Z= 0.205 Angle : 0.796 15.759 47821 Z= 0.385 Chirality : 0.056 0.629 5505 Planarity : 0.005 0.056 5856 Dihedral : 12.035 168.247 5401 Min Nonbonded Distance : 1.078 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.73 % Rotamer: Outliers : 2.92 % Allowed : 19.65 % Favored : 77.43 % 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 are not related in a simple way. whole: -2.43 (0.13), residues: 4144 helix: -0.85 (0.14), residues: 1289 sheet: -0.82 (0.22), residues: 585 loop : -2.36 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 180 TYR 0.038 0.002 TYR D 11 PHE 0.035 0.002 PHE A 56 TRP 0.021 0.002 TRP J 58 HIS 0.014 0.002 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (35025) covalent geometry : angle 0.79576 / 0.38 (47809) SS BOND : bond 0.00437 / 0.22 ( 6) SS BOND : angle 0.81318 / 0.49 ( 12) hydrogen bonds : bond 0.03980 / 2.64 ( 864) hydrogen bonds : angle 5.25620 / 3.66 ( 2380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 466 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 ILE cc_start: 0.7768 (tt) cc_final: 0.7555 (pt) REVERT: C 52 GLU cc_start: 0.8252 (tp30) cc_final: 0.7991 (tp30) REVERT: C 60 ASP cc_start: 0.9015 (m-30) cc_final: 0.8708 (m-30) REVERT: C 131 MET cc_start: 0.8964 (tmm) cc_final: 0.8533 (tmm) REVERT: C 177 ASP cc_start: 0.9006 (p0) cc_final: 0.8136 (t70) REVERT: C 205 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.5697 (mtt) REVERT: D 12 LEU cc_start: 0.9041 (mm) cc_final: 0.8805 (mm) REVERT: D 48 LEU cc_start: 0.8803 (tp) cc_final: 0.8597 (tp) REVERT: E 46 LYS cc_start: 0.9393 (mmmm) cc_final: 0.9044 (mmmm) REVERT: E 53 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5952 (mttm) REVERT: F 46 LYS cc_start: 0.9183 (mttp) cc_final: 0.8936 (mptt) REVERT: G 29 ASP cc_start: 0.8133 (m-30) cc_final: 0.7552 (m-30) REVERT: G 42 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8728 (tm-30) REVERT: G 49 ARG cc_start: 0.9461 (mmm160) cc_final: 0.9222 (mmm160) REVERT: G 72 GLU cc_start: 0.8100 (pm20) cc_final: 0.7842 (pm20) REVERT: H 25 TYR cc_start: 0.8049 (m-10) cc_final: 0.7648 (m-10) REVERT: H 41 LEU cc_start: 0.5922 (mt) cc_final: 0.5275 (pp) REVERT: H 49 ARG cc_start: 0.8750 (ptm160) cc_final: 0.8420 (ptp90) REVERT: I 1 MET cc_start: 0.7393 (mmm) cc_final: 0.7090 (tpp) REVERT: I 63 PHE cc_start: 0.8418 (t80) cc_final: 0.8098 (t80) REVERT: I 246 LEU cc_start: 0.8769 (mm) cc_final: 0.8434 (mp) REVERT: J 119 ASP cc_start: 0.7367 (t0) cc_final: 0.6857 (t0) REVERT: J 184 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7311 (tt) REVERT: J 250 ILE cc_start: 0.9036 (mp) cc_final: 0.8693 (mm) REVERT: J 285 ASP cc_start: 0.7379 (p0) cc_final: 0.7080 (p0) REVERT: K 17 ASN cc_start: 0.7712 (t0) cc_final: 0.7067 (t0) REVERT: K 104 GLN cc_start: 0.8177 (mm110) cc_final: 0.7902 (mm110) REVERT: K 218 ASN cc_start: 0.8104 (m-40) cc_final: 0.7770 (m-40) REVERT: L 54 MET cc_start: 0.7702 (mmp) cc_final: 0.7429 (mmp) REVERT: L 63 PHE cc_start: 0.7975 (t80) cc_final: 0.7637 (t80) REVERT: L 166 ASP cc_start: 0.6058 (t0) cc_final: 0.5500 (p0) REVERT: L 183 MET cc_start: 0.3108 (tpt) cc_final: 0.2883 (mmm) REVERT: L 207 ILE cc_start: 0.8359 (mm) cc_final: 0.8128 (mm) REVERT: L 260 VAL cc_start: 0.8848 (t) cc_final: 0.8632 (t) REVERT: L 283 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5354 (m-80) REVERT: M 1 MET cc_start: 0.7792 (mmm) cc_final: 0.7380 (mtt) REVERT: M 135 LEU cc_start: 0.8215 (mp) cc_final: 0.7993 (mp) REVERT: M 189 TYR cc_start: 0.7999 (m-10) cc_final: 0.7666 (m-10) REVERT: M 211 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8463 (tt) REVERT: M 250 ILE cc_start: 0.8175 (mp) cc_final: 0.7619 (mp) REVERT: M 261 PHE cc_start: 0.8378 (t80) cc_final: 0.7508 (t80) REVERT: N 54 MET cc_start: 0.6094 (mmt) cc_final: 0.5863 (mmt) REVERT: N 59 HIS cc_start: 0.9519 (t-90) cc_final: 0.9284 (t-90) REVERT: N 258 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6951 (t80) REVERT: O 2 TYR cc_start: 0.8102 (m-80) cc_final: 0.7695 (m-80) REVERT: P 10 PHE cc_start: 0.8448 (p90) cc_final: 0.8100 (p90) REVERT: P 12 PHE cc_start: 0.8479 (m-80) cc_final: 0.8075 (m-10) REVERT: P 172 PHE cc_start: 0.8458 (m-80) cc_final: 0.7453 (m-80) REVERT: A 31 MET cc_start: 0.7855 (ptm) cc_final: 0.7576 (ptm) REVERT: A 60 TYR cc_start: 0.7249 (t80) cc_final: 0.6883 (t80) REVERT: A 107 LEU cc_start: 0.9354 (tp) cc_final: 0.9118 (pp) REVERT: A 118 LEU cc_start: 0.8369 (tp) cc_final: 0.8051 (tp) REVERT: A 140 LEU cc_start: 0.8677 (pp) cc_final: 0.8233 (mt) REVERT: A 177 MET cc_start: 0.6388 (mmt) cc_final: 0.5841 (mmt) REVERT: A 236 LEU cc_start: 0.6557 (mm) cc_final: 0.6221 (tp) REVERT: A 246 ASN cc_start: 0.8761 (m110) cc_final: 0.8415 (p0) REVERT: Q 2 SER cc_start: 0.4509 (m) cc_final: 0.4303 (p) REVERT: Q 27 ASN cc_start: 0.8644 (t0) cc_final: 0.8359 (t0) REVERT: Q 37 MET cc_start: 0.8746 (tmm) cc_final: 0.8499 (tmm) REVERT: Q 115 MET cc_start: 0.8791 (mmp) cc_final: 0.8402 (mmm) REVERT: Q 161 LYS cc_start: 0.8529 (mmtm) cc_final: 0.7998 (tmmt) outliers start: 100 outliers final: 61 residues processed: 528 average time/residue: 0.2046 time to fit residues: 179.3471 Evaluate side-chains 484 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 417 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 258 PHE Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain O residue 72 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 178 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 251 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 335 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 GLN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 331 ASN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 ASN O 104 GLN ** O 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 ASN P 213 GLN A 62 ASN A 63 ASN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.080509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066160 restraints weight = 163431.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.068117 restraints weight = 95641.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.069458 restraints weight = 64876.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.070397 restraints weight = 48551.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.071039 restraints weight = 39007.010| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 35031 Z= 0.364 Angle : 0.994 22.594 47821 Z= 0.494 Chirality : 0.060 0.630 5505 Planarity : 0.007 0.070 5856 Dihedral : 12.605 169.317 5401 Min Nonbonded Distance : 0.893 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.74 % Favored : 89.00 % Rotamer: Outliers : 5.36 % Allowed : 19.80 % Favored : 74.84 % 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 are not related in a simple way. whole: -2.87 (0.12), residues: 4144 helix: -1.26 (0.13), residues: 1337 sheet: -1.28 (0.21), residues: 618 loop : -2.57 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 345 TYR 0.035 0.003 TYR M 189 PHE 0.040 0.003 PHE A 56 TRP 0.032 0.003 TRP J 58 HIS 0.018 0.004 HIS K 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.36 (35025) covalent geometry : angle 0.99383 / 0.49 (47809) SS BOND : bond 0.00586 / 0.29 ( 6) SS BOND : angle 1.37164 / 0.77 ( 12) hydrogen bonds : bond 0.05289 / 3.45 ( 864) hydrogen bonds : angle 5.85872 / 4.07 ( 2380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 439 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 ASP cc_start: 0.9130 (m-30) cc_final: 0.8811 (m-30) REVERT: C 111 MET cc_start: 0.7350 (ppp) cc_final: 0.6810 (ppp) REVERT: C 131 MET cc_start: 0.9047 (tmm) cc_final: 0.8761 (tmm) REVERT: C 205 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.5972 (mtt) REVERT: D 12 LEU cc_start: 0.9193 (mm) cc_final: 0.8993 (mm) REVERT: E 46 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9099 (mmmm) REVERT: E 53 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7046 (mttm) REVERT: F 46 LYS cc_start: 0.9180 (mttp) cc_final: 0.8944 (tptt) REVERT: G 21 GLU cc_start: 0.7403 (mp0) cc_final: 0.7004 (mp0) REVERT: G 29 ASP cc_start: 0.8255 (m-30) cc_final: 0.7778 (m-30) REVERT: G 42 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8654 (tm-30) REVERT: G 49 ARG cc_start: 0.9398 (mmm160) cc_final: 0.9110 (mmm160) REVERT: G 99 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8720 (mt) REVERT: H 49 ARG cc_start: 0.8839 (ptm160) cc_final: 0.8482 (ptp90) REVERT: I 63 PHE cc_start: 0.8735 (t80) cc_final: 0.8329 (t80) REVERT: I 104 GLN cc_start: 0.7977 (tp40) cc_final: 0.6537 (tm-30) REVERT: J 104 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7263 (tp-100) REVERT: J 106 ASN cc_start: 0.8583 (m110) cc_final: 0.8359 (p0) REVERT: J 119 ASP cc_start: 0.7665 (t0) cc_final: 0.7100 (t0) REVERT: J 232 LYS cc_start: 0.8780 (tttt) cc_final: 0.8169 (tptt) REVERT: J 285 ASP cc_start: 0.7396 (p0) cc_final: 0.7097 (p0) REVERT: K 17 ASN cc_start: 0.7966 (t0) cc_final: 0.7564 (t0) REVERT: L 2 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: L 63 PHE cc_start: 0.8738 (t80) cc_final: 0.8327 (t80) REVERT: L 166 ASP cc_start: 0.6404 (t0) cc_final: 0.5614 (p0) REVERT: L 215 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: L 235 ILE cc_start: 0.8443 (mm) cc_final: 0.8214 (mm) REVERT: L 239 LEU cc_start: 0.8512 (mt) cc_final: 0.8195 (mt) REVERT: L 283 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.4710 (m-80) REVERT: L 335 MET cc_start: 0.8057 (ppp) cc_final: 0.7642 (ppp) REVERT: M 1 MET cc_start: 0.8120 (mmm) cc_final: 0.7872 (mtt) REVERT: M 19 GLN cc_start: 0.8161 (mp10) cc_final: 0.7361 (mp10) REVERT: M 39 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8065 (tm-30) REVERT: M 135 LEU cc_start: 0.8955 (mp) cc_final: 0.8653 (mp) REVERT: M 194 TYR cc_start: 0.8898 (m-10) cc_final: 0.8101 (m-80) REVERT: M 211 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8502 (tt) REVERT: N 1 MET cc_start: 0.7731 (pmm) cc_final: 0.7491 (pmm) REVERT: N 104 GLN cc_start: 0.8363 (pp30) cc_final: 0.8003 (pp30) REVERT: N 106 ASN cc_start: 0.8359 (m-40) cc_final: 0.8108 (m-40) REVERT: N 156 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7471 (tp) REVERT: N 334 LYS cc_start: 0.8473 (pttt) cc_final: 0.7872 (mmtm) REVERT: O 2 TYR cc_start: 0.8139 (m-80) cc_final: 0.7514 (m-80) REVERT: P 1 MET cc_start: 0.6458 (tpp) cc_final: 0.6245 (tpp) REVERT: P 10 PHE cc_start: 0.8678 (p90) cc_final: 0.8425 (p90) REVERT: P 12 PHE cc_start: 0.8837 (m-80) cc_final: 0.8583 (m-80) REVERT: P 160 PHE cc_start: 0.7895 (m-80) cc_final: 0.7484 (m-80) REVERT: P 172 PHE cc_start: 0.8777 (m-80) cc_final: 0.8160 (m-80) REVERT: P 251 LEU cc_start: 0.7887 (mt) cc_final: 0.7618 (mt) REVERT: A 53 MET cc_start: 0.6360 (ppp) cc_final: 0.6058 (ppp) REVERT: A 63 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.7102 (p0) REVERT: A 107 LEU cc_start: 0.9416 (tp) cc_final: 0.9183 (pp) REVERT: A 140 LEU cc_start: 0.8816 (pp) cc_final: 0.8403 (mm) REVERT: A 177 MET cc_start: 0.6494 (mmt) cc_final: 0.6130 (mmm) REVERT: A 288 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7252 (t0) REVERT: A 610 LEU cc_start: 0.4385 (OUTLIER) cc_final: 0.4164 (tp) REVERT: Q 37 MET cc_start: 0.8946 (tmm) cc_final: 0.8598 (tmm) REVERT: Q 50 ASP cc_start: 0.8269 (m-30) cc_final: 0.8044 (m-30) REVERT: Q 84 HIS cc_start: 0.8367 (p90) cc_final: 0.8109 (p90) REVERT: Q 115 MET cc_start: 0.8742 (mmp) cc_final: 0.8446 (mmt) REVERT: Q 154 SER cc_start: 0.8741 (t) cc_final: 0.8522 (m) REVERT: Q 159 MET cc_start: 0.6459 (pmm) cc_final: 0.6235 (pmm) REVERT: Q 161 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8309 (tmmt) REVERT: Q 192 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8096 (mtp85) outliers start: 184 outliers final: 98 residues processed: 575 average time/residue: 0.1981 time to fit residues: 190.7330 Evaluate side-chains 485 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 376 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain N residue 2 TYR Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 72 TYR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 136 TYR Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 169 LYS Chi-restraints excluded: chain Q residue 178 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 128 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 371 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 338 optimal weight: 0.0170 chunk 210 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 363 optimal weight: 10.0000 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN D 7 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.083757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.069077 restraints weight = 160779.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.071225 restraints weight = 93742.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.072666 restraints weight = 62990.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.073656 restraints weight = 46905.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.074353 restraints weight = 37565.240| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35031 Z= 0.170 Angle : 0.811 14.665 47821 Z= 0.391 Chirality : 0.056 0.633 5505 Planarity : 0.005 0.053 5856 Dihedral : 12.331 162.116 5399 Min Nonbonded Distance : 1.150 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.59 % Favored : 91.17 % Rotamer: Outliers : 3.24 % Allowed : 22.54 % Favored : 74.23 % 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 are not related in a simple way. whole: -2.51 (0.13), residues: 4144 helix: -0.93 (0.14), residues: 1304 sheet: -1.11 (0.22), residues: 603 loop : -2.34 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 180 TYR 0.031 0.002 TYR C 22 PHE 0.025 0.002 PHE A 56 TRP 0.017 0.002 TRP J 58 HIS 0.012 0.002 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (35025) covalent geometry : angle 0.81092 / 0.39 (47809) SS BOND : bond 0.00407 / 0.21 ( 6) SS BOND : angle 0.73061 / 0.46 ( 12) hydrogen bonds : bond 0.03803 / 2.52 ( 864) hydrogen bonds : angle 5.37602 / 3.76 ( 2380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 442 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 ASP cc_start: 0.9072 (m-30) cc_final: 0.8768 (m-30) REVERT: C 65 MET cc_start: 0.9315 (mmt) cc_final: 0.9095 (mmp) REVERT: C 111 MET cc_start: 0.7605 (ppp) cc_final: 0.7195 (ppp) REVERT: C 131 MET cc_start: 0.9118 (tmm) cc_final: 0.8700 (tmm) REVERT: C 205 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.5514 (mtt) REVERT: C 288 PHE cc_start: 0.8986 (t80) cc_final: 0.8715 (t80) REVERT: D 12 LEU cc_start: 0.9212 (mm) cc_final: 0.8772 (mm) REVERT: D 106 ASN cc_start: 0.8248 (m-40) cc_final: 0.8010 (p0) REVERT: E 53 LYS cc_start: 0.6960 (mtpp) cc_final: 0.6636 (mmtp) REVERT: E 92 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9031 (pttm) REVERT: G 29 ASP cc_start: 0.8139 (m-30) cc_final: 0.7580 (m-30) REVERT: G 42 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8651 (tm-30) REVERT: G 49 ARG cc_start: 0.9449 (mmm160) cc_final: 0.9224 (mmm160) REVERT: H 33 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8510 (mtmm) REVERT: H 49 ARG cc_start: 0.8781 (ptm160) cc_final: 0.8439 (ptp90) REVERT: I 54 MET cc_start: 0.8443 (mmm) cc_final: 0.8087 (mmm) REVERT: I 63 PHE cc_start: 0.8513 (t80) cc_final: 0.8141 (t80) REVERT: I 104 GLN cc_start: 0.7990 (tp40) cc_final: 0.6632 (tm-30) REVERT: I 145 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: J 104 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7450 (tm-30) REVERT: J 119 ASP cc_start: 0.7555 (t0) cc_final: 0.7002 (t0) REVERT: J 232 LYS cc_start: 0.8686 (tttt) cc_final: 0.8059 (tptt) REVERT: J 285 ASP cc_start: 0.7396 (p0) cc_final: 0.7112 (p0) REVERT: K 17 ASN cc_start: 0.8025 (t0) cc_final: 0.7639 (t0) REVERT: L 54 MET cc_start: 0.8209 (mmp) cc_final: 0.7902 (mmp) REVERT: L 63 PHE cc_start: 0.8341 (t80) cc_final: 0.8140 (t80) REVERT: L 166 ASP cc_start: 0.6271 (t0) cc_final: 0.5383 (p0) REVERT: L 235 ILE cc_start: 0.8400 (mm) cc_final: 0.8143 (mm) REVERT: L 239 LEU cc_start: 0.8524 (mt) cc_final: 0.8162 (mt) REVERT: L 260 VAL cc_start: 0.9126 (t) cc_final: 0.8925 (t) REVERT: L 283 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.4900 (m-80) REVERT: L 335 MET cc_start: 0.7976 (ppp) cc_final: 0.7408 (ppp) REVERT: M 1 MET cc_start: 0.8191 (mmm) cc_final: 0.7780 (mtt) REVERT: M 9 ILE cc_start: 0.8797 (pt) cc_final: 0.8380 (mm) REVERT: M 19 GLN cc_start: 0.7890 (mp10) cc_final: 0.7111 (mp10) REVERT: M 135 LEU cc_start: 0.8909 (mp) cc_final: 0.8544 (mp) REVERT: M 154 GLU cc_start: 0.8753 (pm20) cc_final: 0.8506 (pm20) REVERT: M 194 TYR cc_start: 0.8678 (m-10) cc_final: 0.8086 (m-80) REVERT: M 211 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8550 (tt) REVERT: N 65 ASP cc_start: 0.8930 (m-30) cc_final: 0.8662 (m-30) REVERT: N 104 GLN cc_start: 0.8328 (pp30) cc_final: 0.7959 (pp30) REVERT: N 328 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9238 (mm) REVERT: N 334 LYS cc_start: 0.8433 (pttt) cc_final: 0.7883 (mmtm) REVERT: O 2 TYR cc_start: 0.8277 (m-80) cc_final: 0.7697 (m-80) REVERT: P 10 PHE cc_start: 0.8433 (p90) cc_final: 0.7984 (p90) REVERT: P 12 PHE cc_start: 0.8656 (m-80) cc_final: 0.8346 (m-80) REVERT: P 137 LEU cc_start: 0.8193 (mm) cc_final: 0.7835 (pp) REVERT: P 141 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7620 (mpp) REVERT: P 172 PHE cc_start: 0.8853 (m-80) cc_final: 0.7775 (m-80) REVERT: P 251 LEU cc_start: 0.8048 (mt) cc_final: 0.7715 (mt) REVERT: A 107 LEU cc_start: 0.9394 (tp) cc_final: 0.9134 (pp) REVERT: A 140 LEU cc_start: 0.8757 (pp) cc_final: 0.8331 (mm) REVERT: A 177 MET cc_start: 0.6542 (mmt) cc_final: 0.5927 (mmt) REVERT: Q 37 MET cc_start: 0.8847 (tmm) cc_final: 0.8603 (tmm) REVERT: Q 115 MET cc_start: 0.8630 (mmp) cc_final: 0.8325 (mmt) REVERT: Q 149 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.4137 (mpp) REVERT: Q 154 SER cc_start: 0.8652 (t) cc_final: 0.8440 (m) REVERT: Q 161 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8208 (tmmt) outliers start: 111 outliers final: 73 residues processed: 524 average time/residue: 0.2048 time to fit residues: 177.5807 Evaluate side-chains 464 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 382 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 243 ILE Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 72 TYR Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 178 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 33 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 384 optimal weight: 0.0770 chunk 265 optimal weight: 5.9990 chunk 399 optimal weight: 8.9990 chunk 262 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 293 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.084225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.069749 restraints weight = 159173.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.071869 restraints weight = 92510.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.073310 restraints weight = 62108.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.074295 restraints weight = 46064.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.074995 restraints weight = 36764.584| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35031 Z= 0.162 Angle : 0.784 14.576 47821 Z= 0.376 Chirality : 0.054 0.555 5505 Planarity : 0.005 0.064 5856 Dihedral : 12.230 162.202 5399 Min Nonbonded Distance : 1.135 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.41 % Favored : 90.37 % Rotamer: Outliers : 3.73 % Allowed : 22.62 % Favored : 73.64 % 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 are not related in a simple way. whole: -2.38 (0.13), residues: 4144 helix: -0.82 (0.14), residues: 1309 sheet: -0.98 (0.22), residues: 584 loop : -2.28 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 10 TYR 0.026 0.002 TYR K 309 PHE 0.026 0.002 PHE N 60 TRP 0.018 0.002 TRP J 58 HIS 0.010 0.002 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (35025) covalent geometry : angle 0.78424 / 0.38 (47809) SS BOND : bond 0.00341 / 0.17 ( 6) SS BOND : angle 0.69377 / 0.41 ( 12) hydrogen bonds : bond 0.03641 / 2.43 ( 864) hydrogen bonds : angle 5.25089 / 3.68 ( 2380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 414 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8561 (mm) REVERT: C 60 ASP cc_start: 0.9045 (m-30) cc_final: 0.8764 (m-30) REVERT: C 111 MET cc_start: 0.7528 (ppp) cc_final: 0.7118 (ppp) REVERT: C 131 MET cc_start: 0.9067 (tmm) cc_final: 0.8607 (tmm) REVERT: C 138 MET cc_start: 0.6697 (mmp) cc_final: 0.6344 (mmp) REVERT: C 185 GLN cc_start: 0.8605 (pm20) cc_final: 0.8361 (pm20) REVERT: C 205 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.5400 (mtt) REVERT: C 297 THR cc_start: 0.8697 (m) cc_final: 0.8390 (p) REVERT: D 12 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8922 (mm) REVERT: D 106 ASN cc_start: 0.8189 (m-40) cc_final: 0.7896 (p0) REVERT: E 53 LYS cc_start: 0.7170 (mtpp) cc_final: 0.6890 (mmtp) REVERT: F 46 LYS cc_start: 0.8951 (mttp) cc_final: 0.8731 (tptt) REVERT: G 29 ASP cc_start: 0.8178 (m-30) cc_final: 0.7687 (m-30) REVERT: G 42 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8637 (tm-30) REVERT: G 49 ARG cc_start: 0.9468 (mmm160) cc_final: 0.9241 (mmm160) REVERT: G 53 LYS cc_start: 0.8874 (tppt) cc_final: 0.8465 (tppt) REVERT: H 29 ASP cc_start: 0.8501 (t70) cc_final: 0.8149 (t0) REVERT: H 33 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8501 (mtmm) REVERT: H 49 ARG cc_start: 0.8764 (ptm160) cc_final: 0.8420 (ptp90) REVERT: I 54 MET cc_start: 0.8509 (mmm) cc_final: 0.8037 (mmm) REVERT: I 63 PHE cc_start: 0.8408 (t80) cc_final: 0.8131 (t80) REVERT: I 104 GLN cc_start: 0.8019 (tp40) cc_final: 0.6669 (tm-30) REVERT: I 145 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: J 119 ASP cc_start: 0.7559 (t0) cc_final: 0.6985 (t0) REVERT: J 232 LYS cc_start: 0.8676 (tttt) cc_final: 0.8035 (tptt) REVERT: J 285 ASP cc_start: 0.7341 (p0) cc_final: 0.7059 (p0) REVERT: J 335 MET cc_start: 0.7345 (ppp) cc_final: 0.6873 (ppp) REVERT: K 17 ASN cc_start: 0.7927 (t0) cc_final: 0.7644 (t0) REVERT: K 202 LEU cc_start: 0.7783 (mp) cc_final: 0.7549 (mp) REVERT: L 54 MET cc_start: 0.8052 (mmp) cc_final: 0.7562 (mmp) REVERT: L 166 ASP cc_start: 0.6083 (t0) cc_final: 0.5325 (p0) REVERT: L 283 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.4986 (m-80) REVERT: L 335 MET cc_start: 0.7898 (ppp) cc_final: 0.7323 (ppp) REVERT: M 1 MET cc_start: 0.8285 (mmm) cc_final: 0.7656 (mtt) REVERT: M 135 LEU cc_start: 0.8870 (mp) cc_final: 0.8496 (mp) REVERT: M 154 GLU cc_start: 0.8627 (pm20) cc_final: 0.8356 (pm20) REVERT: M 194 TYR cc_start: 0.8653 (m-10) cc_final: 0.7634 (m-10) REVERT: M 261 PHE cc_start: 0.8836 (t80) cc_final: 0.8120 (t80) REVERT: M 275 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8067 (mm) REVERT: N 65 ASP cc_start: 0.9015 (m-30) cc_final: 0.8776 (m-30) REVERT: N 104 GLN cc_start: 0.8150 (pp30) cc_final: 0.7916 (pp30) REVERT: N 162 HIS cc_start: 0.5248 (m170) cc_final: 0.4866 (m-70) REVERT: N 334 LYS cc_start: 0.8437 (pttt) cc_final: 0.7922 (mmtm) REVERT: O 2 TYR cc_start: 0.8272 (m-80) cc_final: 0.7711 (m-80) REVERT: O 102 THR cc_start: 0.7751 (m) cc_final: 0.7503 (t) REVERT: P 10 PHE cc_start: 0.8364 (p90) cc_final: 0.7970 (p90) REVERT: P 12 PHE cc_start: 0.8631 (m-80) cc_final: 0.8385 (m-80) REVERT: P 28 LEU cc_start: 0.9132 (mp) cc_final: 0.8926 (mm) REVERT: P 71 VAL cc_start: 0.6348 (OUTLIER) cc_final: 0.6093 (p) REVERT: P 87 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7951 (t0) REVERT: P 137 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7875 (pp) REVERT: P 172 PHE cc_start: 0.8841 (m-80) cc_final: 0.7784 (m-80) REVERT: P 251 LEU cc_start: 0.8006 (mt) cc_final: 0.7665 (mt) REVERT: A 36 LYS cc_start: 0.8983 (tptt) cc_final: 0.7959 (tptt) REVERT: A 107 LEU cc_start: 0.9395 (tp) cc_final: 0.9136 (pp) REVERT: A 140 LEU cc_start: 0.8712 (pp) cc_final: 0.8307 (mm) REVERT: A 159 GLN cc_start: 0.8906 (pm20) cc_final: 0.8667 (pm20) REVERT: A 177 MET cc_start: 0.6512 (mmt) cc_final: 0.5884 (mmt) REVERT: Q 37 MET cc_start: 0.8876 (tmm) cc_final: 0.8595 (tmm) REVERT: Q 115 MET cc_start: 0.8583 (mmp) cc_final: 0.8234 (mmt) REVERT: Q 154 SER cc_start: 0.8489 (t) cc_final: 0.8276 (m) REVERT: Q 161 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8205 (tmmt) outliers start: 128 outliers final: 85 residues processed: 507 average time/residue: 0.2032 time to fit residues: 172.3712 Evaluate side-chains 480 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 385 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 2 TYR Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain O residue 72 TYR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 87 ASN Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 169 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 62 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 347 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 chunk 36 optimal weight: 0.0970 chunk 153 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 368 optimal weight: 8.9990 overall best weight: 1.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.084104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.069707 restraints weight = 159215.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.071818 restraints weight = 92507.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073228 restraints weight = 62098.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.074232 restraints weight = 46096.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.074902 restraints weight = 36667.903| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35031 Z= 0.160 Angle : 0.785 15.042 47821 Z= 0.373 Chirality : 0.054 0.519 5505 Planarity : 0.005 0.062 5856 Dihedral : 12.172 159.168 5399 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % Rotamer: Outliers : 3.38 % Allowed : 22.92 % Favored : 73.70 % 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 are not related in a simple way. whole: -2.38 (0.13), residues: 4144 helix: -0.79 (0.14), residues: 1317 sheet: -1.06 (0.21), residues: 610 loop : -2.28 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 164 TYR 0.020 0.002 TYR C 20 PHE 0.034 0.002 PHE C 288 TRP 0.018 0.002 TRP J 58 HIS 0.009 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (35025) covalent geometry : angle 0.78547 / 0.37 (47809) SS BOND : bond 0.00319 / 0.16 ( 6) SS BOND : angle 0.65138 / 0.39 ( 12) hydrogen bonds : bond 0.03607 / 2.40 ( 864) hydrogen bonds : angle 5.20450 / 3.65 ( 2380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 404 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8550 (mm) REVERT: C 111 MET cc_start: 0.7544 (ppp) cc_final: 0.7150 (ppp) REVERT: C 131 MET cc_start: 0.9045 (tmm) cc_final: 0.8590 (tmm) REVERT: C 205 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.5583 (mtt) REVERT: D 12 LEU cc_start: 0.9099 (mm) cc_final: 0.8891 (mm) REVERT: D 38 GLU cc_start: 0.8299 (pt0) cc_final: 0.7452 (tm-30) REVERT: D 106 ASN cc_start: 0.8152 (m-40) cc_final: 0.7898 (p0) REVERT: E 53 LYS cc_start: 0.7220 (mtpp) cc_final: 0.6997 (mmtp) REVERT: F 46 LYS cc_start: 0.8975 (mttp) cc_final: 0.8733 (tptt) REVERT: G 21 GLU cc_start: 0.6834 (mp0) cc_final: 0.6473 (mp0) REVERT: G 29 ASP cc_start: 0.8200 (m-30) cc_final: 0.7685 (m-30) REVERT: G 42 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8739 (tm-30) REVERT: G 49 ARG cc_start: 0.9476 (mmm160) cc_final: 0.9252 (mmm160) REVERT: G 53 LYS cc_start: 0.8859 (tppt) cc_final: 0.8468 (tppt) REVERT: G 54 LEU cc_start: 0.7654 (mt) cc_final: 0.7273 (mp) REVERT: G 72 GLU cc_start: 0.7939 (pm20) cc_final: 0.7565 (pm20) REVERT: H 29 ASP cc_start: 0.8470 (t70) cc_final: 0.8112 (t0) REVERT: H 33 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8496 (mtmm) REVERT: H 49 ARG cc_start: 0.8778 (ptm160) cc_final: 0.8444 (ptp90) REVERT: I 54 MET cc_start: 0.8542 (mmm) cc_final: 0.8047 (mmm) REVERT: I 63 PHE cc_start: 0.8353 (t80) cc_final: 0.8111 (t80) REVERT: I 104 GLN cc_start: 0.8038 (tp40) cc_final: 0.6673 (tm-30) REVERT: I 145 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: I 246 LEU cc_start: 0.8877 (mm) cc_final: 0.8451 (mp) REVERT: J 119 ASP cc_start: 0.7554 (t0) cc_final: 0.6996 (t0) REVERT: J 232 LYS cc_start: 0.8658 (tttt) cc_final: 0.8052 (tptt) REVERT: J 285 ASP cc_start: 0.7379 (p0) cc_final: 0.7034 (p0) REVERT: J 335 MET cc_start: 0.7430 (ppp) cc_final: 0.6959 (ppp) REVERT: K 17 ASN cc_start: 0.7955 (t0) cc_final: 0.7691 (t0) REVERT: L 54 MET cc_start: 0.7994 (mmp) cc_final: 0.7709 (mmp) REVERT: L 166 ASP cc_start: 0.6027 (t0) cc_final: 0.5278 (p0) REVERT: L 239 LEU cc_start: 0.8398 (mt) cc_final: 0.8150 (tp) REVERT: L 283 TYR cc_start: 0.6393 (OUTLIER) cc_final: 0.5102 (m-80) REVERT: L 335 MET cc_start: 0.7923 (ppp) cc_final: 0.7274 (ppp) REVERT: M 1 MET cc_start: 0.8264 (mmm) cc_final: 0.7732 (mtt) REVERT: M 10 ARG cc_start: 0.7383 (ttm170) cc_final: 0.7148 (ttm170) REVERT: M 19 GLN cc_start: 0.7913 (mp10) cc_final: 0.7167 (mp10) REVERT: M 135 LEU cc_start: 0.8872 (mp) cc_final: 0.8491 (mp) REVERT: M 194 TYR cc_start: 0.8595 (m-10) cc_final: 0.8377 (m-80) REVERT: M 261 PHE cc_start: 0.8827 (t80) cc_final: 0.8159 (t80) REVERT: M 275 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8096 (mm) REVERT: N 65 ASP cc_start: 0.9011 (m-30) cc_final: 0.8735 (m-30) REVERT: N 162 HIS cc_start: 0.5279 (m170) cc_final: 0.5016 (m-70) REVERT: N 328 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9273 (mm) REVERT: N 334 LYS cc_start: 0.8458 (pttt) cc_final: 0.7968 (mmtm) REVERT: O 2 TYR cc_start: 0.8267 (m-80) cc_final: 0.7697 (m-80) REVERT: P 10 PHE cc_start: 0.8357 (p90) cc_final: 0.7880 (p90) REVERT: P 12 PHE cc_start: 0.8575 (m-80) cc_final: 0.8283 (m-80) REVERT: P 71 VAL cc_start: 0.6426 (OUTLIER) cc_final: 0.6123 (p) REVERT: P 87 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8170 (t0) REVERT: P 89 PHE cc_start: 0.7981 (m-10) cc_final: 0.7422 (m-10) REVERT: P 195 MET cc_start: 0.8006 (ppp) cc_final: 0.7652 (ppp) REVERT: P 251 LEU cc_start: 0.8045 (mt) cc_final: 0.7641 (tt) REVERT: A 31 MET cc_start: 0.7266 (ptm) cc_final: 0.6914 (ptm) REVERT: A 36 LYS cc_start: 0.8980 (tptt) cc_final: 0.7960 (tptt) REVERT: A 107 LEU cc_start: 0.9397 (tp) cc_final: 0.9140 (pp) REVERT: A 140 LEU cc_start: 0.8706 (pp) cc_final: 0.8311 (mm) REVERT: A 159 GLN cc_start: 0.8921 (pm20) cc_final: 0.8710 (pm20) REVERT: A 177 MET cc_start: 0.6497 (mmt) cc_final: 0.5867 (mmt) REVERT: A 496 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: Q 37 MET cc_start: 0.8851 (tmm) cc_final: 0.8579 (tmm) REVERT: Q 82 PHE cc_start: 0.6773 (t80) cc_final: 0.6506 (t80) REVERT: Q 115 MET cc_start: 0.8641 (mmp) cc_final: 0.8286 (mmt) REVERT: Q 154 SER cc_start: 0.8554 (t) cc_final: 0.8322 (m) REVERT: Q 161 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8246 (tmmt) outliers start: 116 outliers final: 89 residues processed: 491 average time/residue: 0.2022 time to fit residues: 166.7959 Evaluate side-chains 480 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 381 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 2 TYR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 72 TYR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 87 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 169 LYS Chi-restraints excluded: chain Q residue 178 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 372 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 359 optimal weight: 0.2980 chunk 369 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.079906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.065642 restraints weight = 160540.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067662 restraints weight = 92495.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.069024 restraints weight = 61775.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.069958 restraints weight = 45785.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.070617 restraints weight = 36575.939| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 35031 Z= 0.256 Angle : 0.851 13.796 47821 Z= 0.415 Chirality : 0.055 0.527 5505 Planarity : 0.005 0.075 5856 Dihedral : 12.376 162.200 5399 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.04 % Favored : 89.70 % Rotamer: Outliers : 3.50 % Allowed : 23.32 % Favored : 73.18 % 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 are not related in a simple way. whole: -2.47 (0.13), residues: 4144 helix: -0.81 (0.14), residues: 1332 sheet: -1.17 (0.21), residues: 628 loop : -2.37 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 221 TYR 0.054 0.002 TYR I 72 PHE 0.040 0.003 PHE A 56 TRP 0.028 0.002 TRP J 58 HIS 0.010 0.002 HIS N 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.26 (35025) covalent geometry : angle 0.85090 / 0.41 (47809) SS BOND : bond 0.00369 / 0.19 ( 6) SS BOND : angle 0.80421 / 0.46 ( 12) hydrogen bonds : bond 0.04009 / 2.64 ( 864) hydrogen bonds : angle 5.38098 / 3.77 ( 2380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 387 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 MET cc_start: 0.7639 (ppp) cc_final: 0.7191 (ppp) REVERT: C 131 MET cc_start: 0.9077 (tmm) cc_final: 0.8558 (tmm) REVERT: C 138 MET cc_start: 0.6931 (mmp) cc_final: 0.6681 (mmm) REVERT: C 205 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.5548 (mtt) REVERT: E 53 LYS cc_start: 0.7600 (mtpp) cc_final: 0.7303 (mttm) REVERT: G 21 GLU cc_start: 0.7316 (mp0) cc_final: 0.6867 (mp0) REVERT: G 29 ASP cc_start: 0.8373 (m-30) cc_final: 0.7849 (m-30) REVERT: G 42 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8638 (tm-30) REVERT: G 49 ARG cc_start: 0.9421 (mmm160) cc_final: 0.9154 (mmm160) REVERT: G 53 LYS cc_start: 0.8901 (tppt) cc_final: 0.8287 (tppt) REVERT: G 72 GLU cc_start: 0.8123 (pm20) cc_final: 0.7812 (pm20) REVERT: H 29 ASP cc_start: 0.8548 (t70) cc_final: 0.8217 (t70) REVERT: H 33 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8440 (mtmm) REVERT: H 49 ARG cc_start: 0.8819 (ptm160) cc_final: 0.8501 (ptp90) REVERT: I 54 MET cc_start: 0.8636 (mmm) cc_final: 0.8187 (mmm) REVERT: I 63 PHE cc_start: 0.8641 (t80) cc_final: 0.8265 (t80) REVERT: I 104 GLN cc_start: 0.7824 (tp40) cc_final: 0.6700 (tm-30) REVERT: I 145 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: J 119 ASP cc_start: 0.7916 (t0) cc_final: 0.7470 (t0) REVERT: J 232 LYS cc_start: 0.8583 (tttt) cc_final: 0.8020 (tptt) REVERT: J 285 ASP cc_start: 0.7430 (p0) cc_final: 0.7129 (p0) REVERT: J 335 MET cc_start: 0.7688 (ppp) cc_final: 0.7154 (ppp) REVERT: K 17 ASN cc_start: 0.8076 (t0) cc_final: 0.7785 (t0) REVERT: K 54 MET cc_start: 0.9234 (tpp) cc_final: 0.8969 (tpp) REVERT: L 54 MET cc_start: 0.8423 (mmp) cc_final: 0.8172 (mmp) REVERT: L 166 ASP cc_start: 0.6242 (t0) cc_final: 0.5476 (p0) REVERT: L 215 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7802 (m-10) REVERT: L 239 LEU cc_start: 0.8894 (mt) cc_final: 0.8223 (tt) REVERT: L 283 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5140 (m-80) REVERT: L 335 MET cc_start: 0.8218 (ppp) cc_final: 0.7712 (ppp) REVERT: M 1 MET cc_start: 0.8409 (mmm) cc_final: 0.7850 (mtt) REVERT: M 19 GLN cc_start: 0.8087 (mp10) cc_final: 0.7326 (mp10) REVERT: M 135 LEU cc_start: 0.9001 (mp) cc_final: 0.8687 (mp) REVERT: M 261 PHE cc_start: 0.8902 (t80) cc_final: 0.8227 (t80) REVERT: M 275 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8348 (mm) REVERT: N 65 ASP cc_start: 0.9025 (m-30) cc_final: 0.8765 (m-30) REVERT: N 328 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9226 (mm) REVERT: N 334 LYS cc_start: 0.8536 (pttt) cc_final: 0.8048 (mmtm) REVERT: O 2 TYR cc_start: 0.8272 (m-80) cc_final: 0.7596 (m-80) REVERT: O 198 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8544 (mm) REVERT: P 10 PHE cc_start: 0.8536 (p90) cc_final: 0.8243 (p90) REVERT: P 12 PHE cc_start: 0.8676 (m-80) cc_final: 0.8457 (m-80) REVERT: P 89 PHE cc_start: 0.8249 (m-10) cc_final: 0.7949 (m-10) REVERT: A 31 MET cc_start: 0.7414 (ptm) cc_final: 0.7107 (ptm) REVERT: A 107 LEU cc_start: 0.9404 (tp) cc_final: 0.9154 (pp) REVERT: A 140 LEU cc_start: 0.8794 (pp) cc_final: 0.8398 (mm) REVERT: A 177 MET cc_start: 0.6679 (mmt) cc_final: 0.6172 (mmm) REVERT: A 496 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: Q 115 MET cc_start: 0.8712 (mmp) cc_final: 0.8228 (mmt) REVERT: Q 121 LEU cc_start: 0.8331 (tp) cc_final: 0.8066 (tp) REVERT: Q 154 SER cc_start: 0.8480 (t) cc_final: 0.8212 (m) REVERT: Q 161 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8262 (tmmt) outliers start: 120 outliers final: 89 residues processed: 480 average time/residue: 0.2100 time to fit residues: 167.0902 Evaluate side-chains 459 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 361 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 14 HIS Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 243 ILE Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 2 TYR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 72 TYR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 136 TYR Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 169 LYS Chi-restraints excluded: chain Q residue 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 36 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 257 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 410 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 412 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS J 57 HIS ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 ASN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.081386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.067121 restraints weight = 159928.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.069177 restraints weight = 92227.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.070554 restraints weight = 61567.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.071513 restraints weight = 45506.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.072191 restraints weight = 36198.881| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35031 Z= 0.177 Angle : 0.822 14.222 47821 Z= 0.392 Chirality : 0.054 0.496 5505 Planarity : 0.005 0.064 5856 Dihedral : 12.335 157.913 5399 Min Nonbonded Distance : 1.151 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.93 % Favored : 90.78 % Rotamer: Outliers : 2.83 % Allowed : 24.26 % Favored : 72.92 % 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 are not related in a simple way. whole: -2.41 (0.13), residues: 4144 helix: -0.74 (0.14), residues: 1332 sheet: -1.22 (0.21), residues: 624 loop : -2.33 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 4 TYR 0.027 0.002 TYR K 309 PHE 0.034 0.002 PHE N 60 TRP 0.021 0.002 TRP G 100 HIS 0.009 0.002 HIS N 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (35025) covalent geometry : angle 0.82186 / 0.39 (47809) SS BOND : bond 0.00359 / 0.19 ( 6) SS BOND : angle 0.69238 / 0.41 ( 12) hydrogen bonds : bond 0.03645 / 2.42 ( 864) hydrogen bonds : angle 5.29128 / 3.71 ( 2380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 391 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 MET cc_start: 0.7488 (ppp) cc_final: 0.7058 (ppp) REVERT: C 131 MET cc_start: 0.9078 (tmm) cc_final: 0.8586 (tmm) REVERT: C 138 MET cc_start: 0.6811 (mmp) cc_final: 0.6369 (mmp) REVERT: C 185 GLN cc_start: 0.8390 (pm20) cc_final: 0.8189 (pm20) REVERT: C 205 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.5518 (mtt) REVERT: D 38 GLU cc_start: 0.8322 (pt0) cc_final: 0.7453 (tm-30) REVERT: D 106 ASN cc_start: 0.8197 (m-40) cc_final: 0.7930 (p0) REVERT: E 53 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7425 (mmtp) REVERT: F 42 GLU cc_start: 0.8219 (mp0) cc_final: 0.7740 (pm20) REVERT: G 21 GLU cc_start: 0.7145 (mp0) cc_final: 0.6672 (mp0) REVERT: G 29 ASP cc_start: 0.8363 (m-30) cc_final: 0.7712 (m-30) REVERT: G 42 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8665 (tm-30) REVERT: G 49 ARG cc_start: 0.9434 (mmm160) cc_final: 0.9183 (mmm160) REVERT: G 53 LYS cc_start: 0.8864 (tppt) cc_final: 0.8243 (tppt) REVERT: G 72 GLU cc_start: 0.8068 (pm20) cc_final: 0.7737 (pm20) REVERT: H 12 LEU cc_start: 0.8685 (pp) cc_final: 0.8064 (tp) REVERT: H 29 ASP cc_start: 0.8539 (t70) cc_final: 0.8247 (t70) REVERT: H 33 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8480 (mtmm) REVERT: H 49 ARG cc_start: 0.8813 (ptm160) cc_final: 0.8493 (ptp90) REVERT: I 54 MET cc_start: 0.8557 (mmm) cc_final: 0.8087 (mmm) REVERT: I 63 PHE cc_start: 0.8515 (t80) cc_final: 0.8198 (t80) REVERT: I 104 GLN cc_start: 0.7806 (tp40) cc_final: 0.6711 (tm-30) REVERT: I 145 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: I 246 LEU cc_start: 0.8922 (mm) cc_final: 0.8520 (mp) REVERT: J 119 ASP cc_start: 0.7792 (t0) cc_final: 0.7348 (t0) REVERT: J 285 ASP cc_start: 0.7354 (p0) cc_final: 0.7030 (p0) REVERT: J 335 MET cc_start: 0.7618 (ppp) cc_final: 0.7112 (ppp) REVERT: K 54 MET cc_start: 0.9146 (tpp) cc_final: 0.8843 (tpp) REVERT: L 54 MET cc_start: 0.8117 (mmp) cc_final: 0.7857 (mmp) REVERT: L 239 LEU cc_start: 0.9002 (mt) cc_final: 0.8334 (tt) REVERT: L 283 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.5066 (m-80) REVERT: L 335 MET cc_start: 0.8157 (ppp) cc_final: 0.7651 (ppp) REVERT: M 1 MET cc_start: 0.8362 (mmm) cc_final: 0.7841 (mtt) REVERT: M 19 GLN cc_start: 0.7996 (mp10) cc_final: 0.7264 (mp10) REVERT: M 135 LEU cc_start: 0.8979 (mp) cc_final: 0.8680 (mp) REVERT: M 169 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: M 194 TYR cc_start: 0.8560 (m-80) cc_final: 0.8337 (m-80) REVERT: M 275 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8287 (mm) REVERT: N 65 ASP cc_start: 0.9041 (m-30) cc_final: 0.8748 (m-30) REVERT: N 90 GLN cc_start: 0.7568 (mm110) cc_final: 0.6878 (mp10) REVERT: N 328 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9186 (mm) REVERT: N 334 LYS cc_start: 0.8495 (pttt) cc_final: 0.8074 (mmtm) REVERT: O 2 TYR cc_start: 0.8185 (m-80) cc_final: 0.7596 (m-80) REVERT: O 198 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8469 (mm) REVERT: P 10 PHE cc_start: 0.8375 (p90) cc_final: 0.8110 (p90) REVERT: P 172 PHE cc_start: 0.8853 (m-80) cc_final: 0.8570 (m-80) REVERT: A 31 MET cc_start: 0.7423 (ptm) cc_final: 0.7138 (ptm) REVERT: A 36 LYS cc_start: 0.9032 (tptt) cc_final: 0.8070 (tptt) REVERT: A 91 TYR cc_start: 0.8276 (t80) cc_final: 0.8030 (t80) REVERT: A 107 LEU cc_start: 0.9393 (tp) cc_final: 0.9132 (pp) REVERT: A 140 LEU cc_start: 0.8758 (pp) cc_final: 0.8385 (mm) REVERT: A 177 MET cc_start: 0.6605 (mmt) cc_final: 0.5950 (mmt) REVERT: A 496 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: Q 114 MET cc_start: 0.9058 (ppp) cc_final: 0.8781 (ppp) REVERT: Q 115 MET cc_start: 0.8476 (mmp) cc_final: 0.8148 (mmt) REVERT: Q 121 LEU cc_start: 0.8410 (tp) cc_final: 0.8137 (tp) REVERT: Q 154 SER cc_start: 0.8440 (t) cc_final: 0.8175 (m) REVERT: Q 161 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8237 (tmmt) outliers start: 97 outliers final: 77 residues processed: 465 average time/residue: 0.2090 time to fit residues: 161.1077 Evaluate side-chains 462 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 376 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 72 TYR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 169 LYS Chi-restraints excluded: chain Q residue 175 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 248 optimal weight: 7.9990 chunk 226 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 337 optimal weight: 0.9990 chunk 311 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 410 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 316 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.081408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067049 restraints weight = 159332.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.069097 restraints weight = 91851.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.070478 restraints weight = 61529.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.071453 restraints weight = 45587.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.072122 restraints weight = 36232.924| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.258 35031 Z= 0.225 Angle : 0.893 59.200 47821 Z= 0.453 Chirality : 0.053 0.497 5505 Planarity : 0.005 0.084 5856 Dihedral : 12.333 157.935 5399 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.95 % Favored : 90.76 % Rotamer: Outliers : 2.89 % Allowed : 24.14 % Favored : 72.97 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -2.42 (0.13), residues: 4144 helix: -0.74 (0.14), residues: 1332 sheet: -1.23 (0.21), residues: 624 loop : -2.33 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG N 187 TYR 0.024 0.002 TYR K 309 PHE 0.026 0.002 PHE C 282 TRP 0.021 0.002 TRP G 100 HIS 0.061 0.002 HIS N 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (35025) covalent geometry : angle 0.89257 / 0.45 (47809) SS BOND : bond 0.00338 / 0.17 ( 6) SS BOND : angle 0.68691 / 0.41 ( 12) hydrogen bonds : bond 0.03644 / 2.42 ( 864) hydrogen bonds : angle 5.28588 / 3.71 ( 2380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6278.01 seconds wall clock time: 110 minutes 12.36 seconds (6612.36 seconds total)