Starting phenix.real_space_refine on Mon Jul 6 09:40:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tr9_26083/07_2026/7tr9_26083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr9_26083/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tr9_26083/07_2026/7tr9_26083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr9_26083/07_2026/7tr9_26083.map" model { file = "/net/cci-nas-00/data/ceres_data/7tr9_26083/07_2026/7tr9_26083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr9_26083/07_2026/7tr9_26083.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tr9_26083/07_2026/7tr9_26083.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tr9_26083/07_2026/7tr9_26083.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: {'RNA': 45} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 20, 'rna3p': 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 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: 7.39, per 1000 atoms: 0.22 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 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: 4.10 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: 6.50 Time building geometry restraints manager: 4.02 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 1.50e-02 4.44e+03 2.33e+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=" 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 bond pdb=" O3' DG S 47 " pdb=" P DG S 48 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.17e+01 ... (remaining 35020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 46916 2.28 - 4.57: 771 4.57 - 6.85: 107 6.85 - 9.14: 11 9.14 - 11.42: 4 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 - 35.88: 20633 35.88 - 71.75: 319 71.75 - 107.63: 18 107.63 - 143.50: 0 143.50 - 179.38: 5 Dihedral angle restraints: 20975 sinusoidal: 8838 harmonic: 12137 Sorted by residual: dihedral pdb=" O4' U R 3 " pdb=" C1' U R 3 " pdb=" N1 U R 3 " pdb=" C2 U R 3 " ideal model delta sinusoidal sigma weight residual 200.00 46.98 153.02 1 1.50e+01 4.44e-03 8.07e+01 dihedral pdb=" O4' U R 14 " pdb=" C1' U R 14 " pdb=" N1 U R 14 " pdb=" C2 U R 14 " ideal model delta sinusoidal sigma weight residual -128.00 51.38 -179.38 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C R 40 " pdb=" C1' C R 40 " pdb=" N1 C R 40 " pdb=" C2 C R 40 " ideal model delta sinusoidal sigma weight residual -128.00 50.02 -178.02 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 20972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4945 0.077 - 0.154: 521 0.154 - 0.231: 30 0.231 - 0.307: 5 0.307 - 0.384: 4 Chirality restraints: 5505 Sorted by residual: 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 chirality pdb=" C3' DT S 58 " pdb=" C4' DT S 58 " pdb=" O3' DT S 58 " pdb=" C2' DT S 58 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA ILE J 173 " pdb=" N ILE J 173 " pdb=" C ILE J 173 " pdb=" CB ILE J 173 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.87e+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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.130 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.810 ------------------------------------------------------------------------------- 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= 0.184 Angle : 0.675 11.423 47821 Z= 0.386 Chirality : 0.047 0.384 5505 Planarity : 0.004 0.047 5856 Dihedral : 13.064 179.379 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 0.00303 / 0.18 (35025) covalent geometry : angle 0.67536 / 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 : 1.510 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: 0.2373 time to fit residues: 335.2817 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 : 1.303 ------------------------------------------------------------------------------- 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** J 53 ASN J 57 HIS ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 53 ASN ** 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 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4145 r_free = 0.4145 target = 0.098184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.083675 restraints weight = 164527.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.086036 restraints weight = 100472.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.087685 restraints weight = 68873.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.088839 restraints weight = 51143.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.089625 restraints weight = 40495.023| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 35031 Z= 0.232 Angle : 0.764 14.030 47821 Z= 0.393 Chirality : 0.048 0.255 5505 Planarity : 0.006 0.112 5856 Dihedral : 11.680 178.709 5404 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.83 % Favored : 90.83 % Rotamer: Outliers : 2.45 % Allowed : 13.32 % Favored : 84.23 % 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: -2.57 (0.12), residues: 4144 helix: -1.01 (0.14), residues: 1286 sheet: -0.85 (0.22), residues: 574 loop : -2.43 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 345 TYR 0.028 0.002 TYR F 14 PHE 0.044 0.003 PHE I 282 TRP 0.021 0.002 TRP G 105 HIS 0.013 0.002 HIS L 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (35025) covalent geometry : angle 0.76367 / 0.39 (47809) SS BOND : bond 0.02747 / 1.37 ( 6) SS BOND : angle 0.90649 / 0.58 ( 12) hydrogen bonds : bond 0.04830 / 3.17 ( 864) hydrogen bonds : angle 5.44100 / 3.78 ( 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 646 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 562 time to evaluate : 1.285 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: C 56 HIS cc_start: 0.8911 (m-70) cc_final: 0.8306 (m90) REVERT: C 60 ASP cc_start: 0.8900 (m-30) cc_final: 0.8643 (m-30) REVERT: C 131 MET cc_start: 0.8658 (tmm) cc_final: 0.8369 (tmm) REVERT: C 177 ASP cc_start: 0.8755 (p0) cc_final: 0.7848 (t70) REVERT: C 205 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.5622 (mtt) REVERT: C 276 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8377 (ttmt) REVERT: C 304 ILE cc_start: 0.9097 (tp) cc_final: 0.8835 (tp) REVERT: C 308 MET cc_start: 0.7426 (mpp) cc_final: 0.7076 (mpp) REVERT: D 48 LEU cc_start: 0.8150 (tp) cc_final: 0.7899 (tp) REVERT: F 49 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7674 (mmm160) REVERT: G 29 ASP cc_start: 0.8306 (m-30) cc_final: 0.7739 (m-30) REVERT: G 42 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8636 (tm-30) REVERT: G 72 GLU cc_start: 0.7980 (pm20) cc_final: 0.7708 (pm20) REVERT: H 25 TYR cc_start: 0.7721 (m-10) cc_final: 0.7324 (m-10) REVERT: H 57 LYS cc_start: 0.8080 (tmmt) cc_final: 0.7876 (pptt) REVERT: I 1 MET cc_start: 0.7862 (mmm) cc_final: 0.7391 (mmm) REVERT: I 306 VAL cc_start: 0.8863 (t) cc_final: 0.8618 (p) REVERT: J 107 ASP cc_start: 0.7217 (t70) cc_final: 0.6987 (t70) REVERT: J 119 ASP cc_start: 0.7377 (t0) cc_final: 0.6816 (t0) REVERT: J 184 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7430 (tp) REVERT: J 213 VAL cc_start: 0.7740 (m) cc_final: 0.7506 (m) REVERT: J 232 LYS cc_start: 0.8397 (tttt) cc_final: 0.7704 (tptt) REVERT: J 285 ASP cc_start: 0.7289 (p0) cc_final: 0.6950 (p0) REVERT: K 54 MET cc_start: 0.8992 (tpt) cc_final: 0.8669 (tpp) REVERT: L 63 PHE cc_start: 0.7259 (t80) cc_final: 0.6868 (t80) REVERT: L 166 ASP cc_start: 0.5995 (t0) cc_final: 0.5710 (p0) REVERT: L 207 ILE cc_start: 0.7758 (mm) cc_final: 0.7521 (mm) REVERT: M 19 GLN cc_start: 0.8333 (mp10) cc_final: 0.7766 (mp10) REVERT: M 28 GLU cc_start: 0.8198 (pp20) cc_final: 0.7983 (pp20) REVERT: M 60 PHE cc_start: 0.6933 (t80) cc_final: 0.6483 (t80) REVERT: M 63 PHE cc_start: 0.7929 (t80) cc_final: 0.7718 (t80) REVERT: M 88 PHE cc_start: 0.6596 (m-80) cc_final: 0.6203 (m-80) REVERT: M 135 LEU cc_start: 0.7426 (mp) cc_final: 0.7114 (mp) REVERT: M 211 LEU cc_start: 0.8799 (mt) cc_final: 0.8546 (tt) REVERT: N 10 ARG cc_start: 0.6615 (mtp180) cc_final: 0.5999 (mtp180) REVERT: N 59 HIS cc_start: 0.9381 (t-90) cc_final: 0.8891 (t-90) REVERT: N 160 ILE cc_start: 0.8698 (pt) cc_final: 0.8175 (pt) REVERT: N 187 ARG cc_start: 0.5025 (mpp-170) cc_final: 0.3418 (mpp-170) REVERT: N 202 LEU cc_start: 0.8172 (tp) cc_final: 0.7935 (tp) REVERT: N 258 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6640 (t80) REVERT: O 194 TYR cc_start: 0.6723 (m-80) cc_final: 0.6317 (m-80) REVERT: P 10 PHE cc_start: 0.8303 (p90) cc_final: 0.8053 (p90) REVERT: P 89 PHE cc_start: 0.7987 (m-10) cc_final: 0.7771 (m-10) REVERT: P 115 PHE cc_start: 0.7771 (t80) cc_final: 0.7564 (t80) REVERT: P 172 PHE cc_start: 0.7712 (m-80) cc_final: 0.7225 (m-80) REVERT: A 107 LEU cc_start: 0.9408 (tp) cc_final: 0.9124 (pp) REVERT: A 118 LEU cc_start: 0.8280 (tp) cc_final: 0.7964 (tp) REVERT: A 177 MET cc_start: 0.6048 (mmt) cc_final: 0.5715 (mmt) REVERT: A 246 ASN cc_start: 0.8521 (m110) cc_final: 0.8186 (p0) REVERT: A 340 ASP cc_start: 0.8746 (t0) cc_final: 0.8239 (m-30) REVERT: Q 27 ASN cc_start: 0.8756 (t0) cc_final: 0.8435 (t0) REVERT: Q 99 MET cc_start: 0.7026 (ppp) cc_final: 0.6561 (ppp) REVERT: Q 115 MET cc_start: 0.8822 (mmp) cc_final: 0.8427 (mmm) REVERT: Q 161 LYS cc_start: 0.8381 (mmtm) cc_final: 0.7837 (tmmt) outliers start: 84 outliers final: 46 residues processed: 607 average time/residue: 0.2241 time to fit residues: 220.5208 Evaluate side-chains 503 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 453 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 44 VAL 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 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: 9.9990 chunk 353 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 136 optimal weight: 0.0870 chunk 264 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 382 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 414 optimal weight: 7.9990 chunk 386 optimal weight: 40.0000 overall best weight: 3.7564 ------------------------------------------------------------------------------- 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** ** 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 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 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.093020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.078364 restraints weight = 164288.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.080613 restraints weight = 99483.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.082167 restraints weight = 68311.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.083252 restraints weight = 51108.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.084013 restraints weight = 40813.298| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 35031 Z= 0.239 Angle : 0.735 11.928 47821 Z= 0.380 Chirality : 0.047 0.210 5505 Planarity : 0.005 0.066 5856 Dihedral : 11.758 179.738 5401 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.98 % Favored : 90.73 % Rotamer: Outliers : 3.44 % Allowed : 16.76 % Favored : 79.80 % 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 (0.12), residues: 4144 helix: -0.91 (0.14), residues: 1278 sheet: -0.91 (0.22), residues: 591 loop : -2.40 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 87 TYR 0.044 0.002 TYR C 20 PHE 0.030 0.003 PHE J 60 TRP 0.028 0.002 TRP H 105 HIS 0.016 0.002 HIS K 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (35025) covalent geometry : angle 0.73539 / 0.38 (47809) SS BOND : bond 0.00672 / 0.34 ( 6) SS BOND : angle 0.83303 / 0.52 ( 12) hydrogen bonds : bond 0.04671 / 3.15 ( 864) hydrogen bonds : angle 5.31736 / 3.68 ( 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 613 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 495 time to evaluate : 1.178 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 37 ILE cc_start: 0.7131 (tt) cc_final: 0.6931 (pt) REVERT: C 58 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8576 (mm) REVERT: C 60 ASP cc_start: 0.8963 (m-30) cc_final: 0.8674 (m-30) REVERT: C 62 LEU cc_start: 0.8889 (mm) cc_final: 0.8652 (pp) REVERT: C 111 MET cc_start: 0.7533 (ptp) cc_final: 0.7315 (ppp) REVERT: C 177 ASP cc_start: 0.8828 (p0) cc_final: 0.7905 (t70) REVERT: C 205 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.5713 (mtt) REVERT: C 276 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8417 (ttmt) REVERT: C 312 LEU cc_start: 0.9155 (tp) cc_final: 0.8939 (tp) REVERT: D 48 LEU cc_start: 0.8377 (tp) cc_final: 0.8138 (tp) REVERT: E 46 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9054 (mmmm) REVERT: E 53 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5649 (mmtp) REVERT: E 88 LYS cc_start: 0.9143 (tptt) cc_final: 0.8853 (tppt) REVERT: F 46 LYS cc_start: 0.9113 (mttp) cc_final: 0.8894 (mptt) REVERT: G 29 ASP cc_start: 0.8031 (m-30) cc_final: 0.7485 (m-30) REVERT: G 42 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8546 (tm-30) REVERT: G 53 LYS cc_start: 0.8739 (tppt) cc_final: 0.8370 (tppt) REVERT: G 72 GLU cc_start: 0.8027 (pm20) cc_final: 0.7766 (pm20) REVERT: H 25 TYR cc_start: 0.7718 (m-10) cc_final: 0.7230 (m-10) REVERT: H 41 LEU cc_start: 0.5703 (mt) cc_final: 0.5103 (pp) REVERT: I 1 MET cc_start: 0.7420 (mmm) cc_final: 0.6693 (tpp) REVERT: I 306 VAL cc_start: 0.9176 (t) cc_final: 0.8866 (p) REVERT: J 54 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8404 (tpp) REVERT: J 107 ASP cc_start: 0.7528 (t70) cc_final: 0.7315 (t70) REVERT: J 119 ASP cc_start: 0.7387 (t0) cc_final: 0.6915 (t0) REVERT: J 184 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7551 (mt) REVERT: J 213 VAL cc_start: 0.8344 (m) cc_final: 0.8135 (m) REVERT: J 232 LYS cc_start: 0.8539 (tttt) cc_final: 0.7953 (tptt) REVERT: J 285 ASP cc_start: 0.7384 (p0) cc_final: 0.7064 (p0) REVERT: K 54 MET cc_start: 0.9039 (tpt) cc_final: 0.8744 (tpp) REVERT: K 218 ASN cc_start: 0.8014 (m-40) cc_final: 0.7812 (m-40) REVERT: L 25 ASN cc_start: 0.5846 (OUTLIER) cc_final: 0.5209 (t0) REVERT: L 63 PHE cc_start: 0.7547 (t80) cc_final: 0.7212 (t80) REVERT: L 166 ASP cc_start: 0.6153 (t0) cc_final: 0.5705 (p0) REVERT: L 207 ILE cc_start: 0.8004 (mm) cc_final: 0.7677 (mm) REVERT: L 283 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.5049 (m-80) REVERT: M 1 MET cc_start: 0.7692 (mmm) cc_final: 0.6695 (mtt) REVERT: M 9 ILE cc_start: 0.8361 (pt) cc_final: 0.8020 (mm) REVERT: M 60 PHE cc_start: 0.7360 (t80) cc_final: 0.6946 (t80) REVERT: M 135 LEU cc_start: 0.7923 (mp) cc_final: 0.7675 (mp) REVERT: M 196 PHE cc_start: 0.7360 (p90) cc_final: 0.7157 (p90) REVERT: M 261 PHE cc_start: 0.8364 (t80) cc_final: 0.7745 (t80) REVERT: M 318 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7578 (tm-30) REVERT: N 59 HIS cc_start: 0.9464 (t-90) cc_final: 0.9094 (t-90) REVERT: N 162 HIS cc_start: 0.5528 (m170) cc_final: 0.5010 (m170) REVERT: N 258 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6727 (t80) REVERT: O 31 LYS cc_start: 0.7825 (mppt) cc_final: 0.7581 (mmtm) REVERT: O 194 TYR cc_start: 0.6824 (m-80) cc_final: 0.6451 (m-80) REVERT: P 10 PHE cc_start: 0.8389 (p90) cc_final: 0.8002 (p90) REVERT: P 12 PHE cc_start: 0.8091 (m-10) cc_final: 0.7575 (m-80) REVERT: P 89 PHE cc_start: 0.8271 (m-10) cc_final: 0.7117 (m-10) REVERT: P 172 PHE cc_start: 0.8185 (m-80) cc_final: 0.7363 (m-80) REVERT: A 107 LEU cc_start: 0.9344 (tp) cc_final: 0.9118 (pp) REVERT: A 118 LEU cc_start: 0.8419 (tp) cc_final: 0.8073 (tp) REVERT: A 140 LEU cc_start: 0.8632 (pp) cc_final: 0.8016 (mt) REVERT: A 177 MET cc_start: 0.6280 (mmt) cc_final: 0.6031 (mmm) REVERT: A 246 ASN cc_start: 0.8755 (m110) cc_final: 0.8326 (p0) REVERT: A 301 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8056 (tmm-80) REVERT: Q 50 ASP cc_start: 0.8267 (m-30) cc_final: 0.7851 (m-30) REVERT: Q 115 MET cc_start: 0.8767 (mmp) cc_final: 0.8485 (mmm) REVERT: Q 161 LYS cc_start: 0.8397 (mmtm) cc_final: 0.7878 (tmmt) outliers start: 118 outliers final: 65 residues processed: 572 average time/residue: 0.2094 time to fit residues: 196.5235 Evaluate side-chains 520 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 446 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 16 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 45 TYR Chi-restraints excluded: chain E residue 50 LEU 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 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 50 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 54 MET 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 235 ILE Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 312 ASP Chi-restraints excluded: chain L residue 25 ASN 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 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 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 90 GLN 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 91 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 124 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 172 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 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** O 90 GLN P 87 ASN A 328 ASN Q 72 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.091517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.076866 restraints weight = 163136.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.079102 restraints weight = 97888.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.080627 restraints weight = 66788.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.081698 restraints weight = 49907.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.082452 restraints weight = 39882.645| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35031 Z= 0.186 Angle : 0.686 10.021 47821 Z= 0.349 Chirality : 0.045 0.213 5505 Planarity : 0.005 0.055 5856 Dihedral : 11.813 178.974 5401 Min Nonbonded Distance : 1.064 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.27 % Favored : 90.52 % Rotamer: Outliers : 2.71 % Allowed : 19.42 % Favored : 77.87 % 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: -0.83 (0.14), residues: 1287 sheet: -0.73 (0.22), residues: 586 loop : -2.34 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 180 TYR 0.032 0.002 TYR G 45 PHE 0.038 0.002 PHE A 56 TRP 0.020 0.002 TRP J 58 HIS 0.012 0.002 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (35025) covalent geometry : angle 0.68606 / 0.35 (47809) SS BOND : bond 0.00357 / 0.18 ( 6) SS BOND : angle 0.71640 / 0.44 ( 12) hydrogen bonds : bond 0.03916 / 2.60 ( 864) hydrogen bonds : angle 5.21168 / 3.62 ( 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 553 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 460 time to evaluate : 1.203 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: C 52 GLU cc_start: 0.8416 (tp30) cc_final: 0.8158 (tp30) REVERT: C 58 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8599 (mm) REVERT: C 60 ASP cc_start: 0.9016 (m-30) cc_final: 0.8724 (m-30) REVERT: C 62 LEU cc_start: 0.8867 (mm) cc_final: 0.8665 (pp) REVERT: C 131 MET cc_start: 0.8927 (tmm) cc_final: 0.8519 (tmm) REVERT: C 177 ASP cc_start: 0.8959 (p0) cc_final: 0.8048 (t70) REVERT: C 185 GLN cc_start: 0.7578 (pm20) cc_final: 0.7238 (pp30) REVERT: C 205 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.5669 (mtt) REVERT: C 312 LEU cc_start: 0.9159 (tp) cc_final: 0.8947 (tp) REVERT: D 48 LEU cc_start: 0.8505 (tp) cc_final: 0.8268 (tp) REVERT: D 73 ASP cc_start: 0.6587 (p0) cc_final: 0.6346 (p0) REVERT: E 46 LYS cc_start: 0.9390 (mmmm) cc_final: 0.9033 (mmmm) REVERT: E 53 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.6233 (mmmm) REVERT: E 89 ASP cc_start: 0.8271 (p0) cc_final: 0.8066 (p0) REVERT: E 92 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8231 (pttm) REVERT: F 99 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8805 (pt) REVERT: G 29 ASP cc_start: 0.8100 (m-30) cc_final: 0.7604 (m-30) REVERT: G 42 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8735 (tm-30) REVERT: G 49 ARG cc_start: 0.9413 (mmm160) cc_final: 0.9151 (mmm160) REVERT: G 72 GLU cc_start: 0.8111 (pm20) cc_final: 0.7862 (pm20) REVERT: H 29 ASP cc_start: 0.8182 (t0) cc_final: 0.7966 (m-30) REVERT: H 41 LEU cc_start: 0.6069 (mt) cc_final: 0.5462 (pp) REVERT: I 1 MET cc_start: 0.7282 (mmm) cc_final: 0.6657 (tpp) REVERT: I 63 PHE cc_start: 0.8364 (t80) cc_final: 0.8042 (t80) REVERT: I 269 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8697 (pt) REVERT: I 306 VAL cc_start: 0.9306 (t) cc_final: 0.9005 (m) REVERT: J 54 MET cc_start: 0.8815 (tpp) cc_final: 0.8050 (tpp) REVERT: J 119 ASP cc_start: 0.7362 (t0) cc_final: 0.6882 (t0) REVERT: J 135 LEU cc_start: 0.8801 (mm) cc_final: 0.8459 (mm) REVERT: J 184 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7700 (tt) REVERT: J 285 ASP cc_start: 0.7362 (p0) cc_final: 0.7052 (p0) REVERT: K 54 MET cc_start: 0.9084 (tpt) cc_final: 0.8744 (tpp) REVERT: L 63 PHE cc_start: 0.7739 (t80) cc_final: 0.7425 (t80) REVERT: L 166 ASP cc_start: 0.5974 (t0) cc_final: 0.5450 (p0) REVERT: L 207 ILE cc_start: 0.8203 (mm) cc_final: 0.7902 (mm) REVERT: L 283 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.5470 (m-80) REVERT: M 1 MET cc_start: 0.7754 (mmm) cc_final: 0.6705 (mtt) REVERT: M 9 ILE cc_start: 0.8505 (pt) cc_final: 0.8072 (mm) REVERT: M 135 LEU cc_start: 0.8149 (mp) cc_final: 0.7918 (mp) REVERT: M 196 PHE cc_start: 0.7741 (p90) cc_final: 0.7503 (p90) REVERT: M 250 ILE cc_start: 0.8182 (mp) cc_final: 0.7744 (mp) REVERT: M 261 PHE cc_start: 0.8500 (t80) cc_final: 0.7490 (t80) REVERT: M 318 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7578 (tm-30) REVERT: N 59 HIS cc_start: 0.9490 (t-90) cc_final: 0.9213 (t-90) REVERT: N 258 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6866 (t80) REVERT: N 334 LYS cc_start: 0.8147 (pttt) cc_final: 0.7455 (mmtt) REVERT: O 31 LYS cc_start: 0.7777 (mppt) cc_final: 0.7532 (mmtm) REVERT: P 10 PHE cc_start: 0.8369 (p90) cc_final: 0.8051 (p90) REVERT: P 12 PHE cc_start: 0.8009 (m-10) cc_final: 0.7727 (m-10) REVERT: P 89 PHE cc_start: 0.8236 (m-10) cc_final: 0.7953 (m-10) REVERT: P 172 PHE cc_start: 0.8388 (m-80) cc_final: 0.7453 (m-80) REVERT: A 31 MET cc_start: 0.7828 (ptm) cc_final: 0.7535 (ptm) REVERT: A 60 TYR cc_start: 0.7164 (t80) cc_final: 0.6749 (t80) REVERT: A 107 LEU cc_start: 0.9352 (tp) cc_final: 0.9113 (pp) REVERT: A 118 LEU cc_start: 0.8414 (tp) cc_final: 0.8044 (tp) REVERT: A 140 LEU cc_start: 0.8654 (pp) cc_final: 0.8125 (mt) REVERT: A 177 MET cc_start: 0.6363 (mmt) cc_final: 0.5823 (mmt) REVERT: A 236 LEU cc_start: 0.6387 (mm) cc_final: 0.6116 (tp) REVERT: A 246 ASN cc_start: 0.8759 (m110) cc_final: 0.8405 (p0) REVERT: Q 2 SER cc_start: 0.4628 (m) cc_final: 0.4389 (p) REVERT: Q 27 ASN cc_start: 0.8547 (t0) cc_final: 0.8261 (t0) REVERT: Q 50 ASP cc_start: 0.8350 (m-30) cc_final: 0.8134 (m-30) REVERT: Q 99 MET cc_start: 0.7480 (ppp) cc_final: 0.7049 (ppp) REVERT: Q 115 MET cc_start: 0.8793 (mmp) cc_final: 0.8507 (mmm) REVERT: Q 161 LYS cc_start: 0.8516 (mmtm) cc_final: 0.7959 (tmmt) REVERT: Q 169 LYS cc_start: 0.0769 (OUTLIER) cc_final: -0.1346 (ptmm) outliers start: 93 outliers final: 52 residues processed: 519 average time/residue: 0.1938 time to fit residues: 167.3304 Evaluate side-chains 480 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 418 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 53 LYS 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 29 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 278 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 304 ILE Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 51 THR 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 184 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 N residue 32 THR 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 310 ASN 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 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 325 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 169 LYS 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: 9.9990 chunk 77 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 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** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** M 121 HIS ** 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 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.087511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.072818 restraints weight = 163914.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.074987 restraints weight = 97209.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.076470 restraints weight = 66120.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.077506 restraints weight = 49374.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.078242 restraints weight = 39449.681| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 35031 Z= 0.228 Angle : 0.717 10.203 47821 Z= 0.368 Chirality : 0.047 0.298 5505 Planarity : 0.005 0.054 5856 Dihedral : 11.949 179.437 5401 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.19 % Favored : 90.59 % Rotamer: Outliers : 3.97 % Allowed : 19.62 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.76 (0.14), residues: 1292 sheet: -0.82 (0.22), residues: 575 loop : -2.35 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 180 TYR 0.034 0.002 TYR A 484 PHE 0.040 0.002 PHE A 56 TRP 0.024 0.002 TRP J 58 HIS 0.013 0.002 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (35025) covalent geometry : angle 0.71652 / 0.37 (47809) SS BOND : bond 0.00366 / 0.19 ( 6) SS BOND : angle 0.73855 / 0.44 ( 12) hydrogen bonds : bond 0.04105 / 2.71 ( 864) hydrogen bonds : angle 5.23423 / 3.63 ( 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 568 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 432 time to evaluate : 1.299 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 60 ASP cc_start: 0.9058 (m-30) cc_final: 0.8767 (m-30) REVERT: C 111 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7473 (ppp) REVERT: C 131 MET cc_start: 0.9012 (tmm) cc_final: 0.8774 (tmm) REVERT: C 177 ASP cc_start: 0.9061 (p0) cc_final: 0.8186 (t70) REVERT: C 205 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.5717 (mtt) REVERT: D 48 LEU cc_start: 0.9010 (tp) cc_final: 0.8762 (tp) REVERT: E 46 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9057 (mmmm) REVERT: E 53 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6350 (mmtp) REVERT: F 99 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8953 (pt) REVERT: G 29 ASP cc_start: 0.8184 (m-30) cc_final: 0.7623 (m-30) REVERT: G 42 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8822 (tm-30) REVERT: H 29 ASP cc_start: 0.8433 (t0) cc_final: 0.8017 (p0) REVERT: H 41 LEU cc_start: 0.6182 (mt) cc_final: 0.5563 (pp) REVERT: I 1 MET cc_start: 0.7685 (mmm) cc_final: 0.7302 (tpp) REVERT: I 31 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7844 (mmtp) REVERT: I 246 LEU cc_start: 0.8817 (mm) cc_final: 0.8493 (mp) REVERT: I 315 GLU cc_start: 0.8102 (pt0) cc_final: 0.7900 (pm20) REVERT: J 54 MET cc_start: 0.8900 (tpp) cc_final: 0.8133 (tpp) REVERT: J 119 ASP cc_start: 0.7443 (t0) cc_final: 0.6894 (t0) REVERT: J 285 ASP cc_start: 0.7480 (p0) cc_final: 0.7177 (p0) REVERT: K 54 MET cc_start: 0.9182 (tpt) cc_final: 0.8867 (tpp) REVERT: L 54 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8171 (mmp) REVERT: L 63 PHE cc_start: 0.8140 (t80) cc_final: 0.7797 (t80) REVERT: L 166 ASP cc_start: 0.6179 (t0) cc_final: 0.5435 (p0) REVERT: L 260 VAL cc_start: 0.8817 (t) cc_final: 0.8579 (t) REVERT: L 283 TYR cc_start: 0.6379 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: M 135 LEU cc_start: 0.8426 (mp) cc_final: 0.8159 (mp) REVERT: M 189 TYR cc_start: 0.8092 (m-10) cc_final: 0.7745 (m-10) REVERT: M 194 TYR cc_start: 0.8712 (m-10) cc_final: 0.7901 (m-80) REVERT: M 261 PHE cc_start: 0.8553 (t80) cc_final: 0.7822 (t80) REVERT: M 318 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7573 (tm-30) REVERT: N 54 MET cc_start: 0.6751 (mmt) cc_final: 0.6535 (mmt) REVERT: N 59 HIS cc_start: 0.9529 (t-90) cc_final: 0.9296 (t-90) REVERT: N 104 GLN cc_start: 0.8221 (pp30) cc_final: 0.8000 (pp30) REVERT: O 2 TYR cc_start: 0.8261 (m-80) cc_final: 0.7849 (m-80) REVERT: P 10 PHE cc_start: 0.8537 (p90) cc_final: 0.8166 (p90) REVERT: P 12 PHE cc_start: 0.8413 (m-10) cc_final: 0.8018 (m-80) REVERT: P 78 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7957 (p) REVERT: P 172 PHE cc_start: 0.8618 (m-80) cc_final: 0.7422 (m-80) REVERT: A 107 LEU cc_start: 0.9366 (tp) cc_final: 0.9131 (pp) REVERT: A 118 LEU cc_start: 0.8421 (tp) cc_final: 0.8143 (tp) REVERT: A 140 LEU cc_start: 0.8694 (pp) cc_final: 0.8262 (mm) REVERT: A 177 MET cc_start: 0.6513 (mmt) cc_final: 0.5969 (mmt) REVERT: A 236 LEU cc_start: 0.6941 (mm) cc_final: 0.6525 (tp) REVERT: A 246 ASN cc_start: 0.8773 (m110) cc_final: 0.8442 (p0) REVERT: Q 2 SER cc_start: 0.4879 (m) cc_final: 0.4670 (p) REVERT: Q 27 ASN cc_start: 0.8724 (t0) cc_final: 0.8424 (t0) REVERT: Q 99 MET cc_start: 0.7891 (ppp) cc_final: 0.7608 (ppp) REVERT: Q 161 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8100 (tmmt) REVERT: Q 169 LYS cc_start: 0.1161 (OUTLIER) cc_final: -0.0954 (ptmm) outliers start: 136 outliers final: 85 residues processed: 516 average time/residue: 0.2056 time to fit residues: 177.1637 Evaluate side-chains 487 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 394 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 111 MET 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 139 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 45 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 14 TYR 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 F residue 99 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 57 LYS 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 200 LEU 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 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 218 ASN 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 329 VAL Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 204 LEU 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 136 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 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 146 ASP Chi-restraints excluded: chain N residue 242 LEU 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 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 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 78 VAL 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 135 LEU Chi-restraints excluded: chain P residue 141 MET 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 243 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain Q residue 25 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: 2.9990 chunk 4 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 371 optimal weight: 0.2980 chunk 217 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 338 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN D 7 ASN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.089680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.074934 restraints weight = 160530.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.077163 restraints weight = 95505.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.078689 restraints weight = 64919.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.079756 restraints weight = 48415.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.080509 restraints weight = 38596.317| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35031 Z= 0.137 Angle : 0.677 10.469 47821 Z= 0.339 Chirality : 0.045 0.280 5505 Planarity : 0.004 0.045 5856 Dihedral : 11.905 179.362 5399 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.40 % Favored : 91.36 % Rotamer: Outliers : 3.50 % Allowed : 20.93 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.31 (0.13), residues: 4144 helix: -0.71 (0.14), residues: 1289 sheet: -0.84 (0.22), residues: 579 loop : -2.28 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 180 TYR 0.037 0.002 TYR D 11 PHE 0.047 0.002 PHE A 56 TRP 0.017 0.001 TRP A 133 HIS 0.013 0.002 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (35025) covalent geometry : angle 0.67722 / 0.34 (47809) SS BOND : bond 0.00328 / 0.16 ( 6) SS BOND : angle 0.57280 / 0.36 ( 12) hydrogen bonds : bond 0.03577 / 2.38 ( 864) hydrogen bonds : angle 5.07961 / 3.53 ( 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 559 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 439 time to evaluate : 1.201 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 58 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8713 (mm) REVERT: C 60 ASP cc_start: 0.8989 (m-30) cc_final: 0.8675 (m-30) REVERT: C 111 MET cc_start: 0.7957 (ptt) cc_final: 0.7682 (ppp) REVERT: C 131 MET cc_start: 0.9040 (tmm) cc_final: 0.8642 (tmm) REVERT: C 177 ASP cc_start: 0.9032 (p0) cc_final: 0.8144 (t70) REVERT: C 205 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.5425 (mtt) REVERT: D 12 LEU cc_start: 0.9087 (mm) cc_final: 0.8752 (mm) REVERT: E 46 LYS cc_start: 0.9385 (mmmm) cc_final: 0.8992 (mmmm) REVERT: E 88 LYS cc_start: 0.8995 (tppt) cc_final: 0.8760 (tppt) REVERT: E 89 ASP cc_start: 0.8217 (p0) cc_final: 0.7833 (p0) REVERT: E 92 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8653 (pttm) REVERT: F 99 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8966 (pt) REVERT: G 29 ASP cc_start: 0.8114 (m-30) cc_final: 0.7474 (m-30) REVERT: G 42 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8796 (tm-30) REVERT: G 49 ARG cc_start: 0.9408 (mmm160) cc_final: 0.9066 (mmm160) REVERT: H 29 ASP cc_start: 0.8423 (t0) cc_final: 0.8028 (p0) REVERT: H 33 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8432 (pttm) REVERT: H 41 LEU cc_start: 0.6260 (mt) cc_final: 0.5677 (pp) REVERT: I 1 MET cc_start: 0.7672 (mmm) cc_final: 0.7197 (tpp) REVERT: I 145 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: J 54 MET cc_start: 0.8752 (tpp) cc_final: 0.7897 (tpp) REVERT: J 119 ASP cc_start: 0.7380 (t0) cc_final: 0.6859 (t0) REVERT: J 135 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8412 (mm) REVERT: J 285 ASP cc_start: 0.7477 (p0) cc_final: 0.7119 (p0) REVERT: L 54 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7709 (mmp) REVERT: L 63 PHE cc_start: 0.8132 (t80) cc_final: 0.7785 (t80) REVERT: L 166 ASP cc_start: 0.6018 (t0) cc_final: 0.5325 (p0) REVERT: L 260 VAL cc_start: 0.8728 (t) cc_final: 0.8527 (t) REVERT: L 283 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.4853 (m-80) REVERT: M 1 MET cc_start: 0.8085 (mmm) cc_final: 0.7509 (mtt) REVERT: M 194 TYR cc_start: 0.8546 (m-10) cc_final: 0.7933 (m-80) REVERT: M 261 PHE cc_start: 0.8642 (t80) cc_final: 0.7784 (t80) REVERT: M 318 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7299 (tm-30) REVERT: N 54 MET cc_start: 0.6674 (mmt) cc_final: 0.6467 (mmt) REVERT: N 59 HIS cc_start: 0.9508 (t-90) cc_final: 0.9287 (t-90) REVERT: N 334 LYS cc_start: 0.8115 (pttm) cc_final: 0.7536 (mmtm) REVERT: O 2 TYR cc_start: 0.8149 (m-80) cc_final: 0.7663 (m-80) REVERT: O 65 ASP cc_start: 0.8886 (m-30) cc_final: 0.8605 (m-30) REVERT: P 10 PHE cc_start: 0.8338 (p90) cc_final: 0.8053 (p90) REVERT: P 109 MET cc_start: 0.8405 (mmt) cc_final: 0.8118 (mtt) REVERT: P 172 PHE cc_start: 0.8594 (m-80) cc_final: 0.7580 (m-80) REVERT: A 48 THR cc_start: 0.7014 (OUTLIER) cc_final: 0.6624 (m) REVERT: A 60 TYR cc_start: 0.7359 (t80) cc_final: 0.7013 (t80) REVERT: A 107 LEU cc_start: 0.9352 (tp) cc_final: 0.9107 (pp) REVERT: A 118 LEU cc_start: 0.8434 (tp) cc_final: 0.8088 (tp) REVERT: A 140 LEU cc_start: 0.8696 (pp) cc_final: 0.8296 (mm) REVERT: A 177 MET cc_start: 0.6442 (mmt) cc_final: 0.5843 (mmt) REVERT: A 236 LEU cc_start: 0.6935 (mm) cc_final: 0.6508 (tp) REVERT: A 246 ASN cc_start: 0.8749 (m110) cc_final: 0.8431 (p0) REVERT: Q 2 SER cc_start: 0.4851 (m) cc_final: 0.4643 (p) REVERT: Q 27 ASN cc_start: 0.8777 (t0) cc_final: 0.8462 (t0) REVERT: Q 50 ASP cc_start: 0.8261 (m-30) cc_final: 0.7942 (t0) REVERT: Q 53 MET cc_start: 0.7506 (ptt) cc_final: 0.6623 (ptt) REVERT: Q 99 MET cc_start: 0.7807 (ppp) cc_final: 0.7439 (ppp) REVERT: Q 161 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8046 (tmmt) REVERT: Q 169 LYS cc_start: 0.0611 (OUTLIER) cc_final: -0.1501 (ptmm) outliers start: 120 outliers final: 69 residues processed: 526 average time/residue: 0.1901 time to fit residues: 166.6996 Evaluate side-chains 477 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 397 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 VAL 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 139 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 7 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 45 TYR 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 74 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 5 ILE 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 3 VAL Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 196 PHE 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 328 LEU Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 2 TYR 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 246 LEU 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 124 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain Q residue 111 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 33 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 384 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 399 optimal weight: 0.0000 chunk 262 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 171 optimal weight: 0.0370 chunk 293 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 0.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN K 162 HIS ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 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 106 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.090146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.075367 restraints weight = 161822.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.077627 restraints weight = 95772.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.079164 restraints weight = 64929.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.080230 restraints weight = 48283.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.080983 restraints weight = 38543.994| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35031 Z= 0.133 Angle : 0.685 13.650 47821 Z= 0.340 Chirality : 0.046 0.249 5505 Planarity : 0.004 0.065 5856 Dihedral : 11.877 179.892 5399 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.69 % Favored : 91.07 % Rotamer: Outliers : 2.92 % Allowed : 21.98 % Favored : 75.10 % 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: -2.29 (0.13), residues: 4144 helix: -0.69 (0.15), residues: 1289 sheet: -0.83 (0.22), residues: 580 loop : -2.28 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 180 TYR 0.037 0.002 TYR G 45 PHE 0.040 0.002 PHE A 56 TRP 0.016 0.001 TRP Q 22 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (35025) covalent geometry : angle 0.68457 / 0.34 (47809) SS BOND : bond 0.00287 / 0.14 ( 6) SS BOND : angle 0.53942 / 0.33 ( 12) hydrogen bonds : bond 0.03479 / 2.31 ( 864) hydrogen bonds : angle 5.05285 / 3.52 ( 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 518 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 418 time to evaluate : 1.089 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 58 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8688 (mm) REVERT: C 60 ASP cc_start: 0.8985 (m-30) cc_final: 0.8697 (m-30) REVERT: C 111 MET cc_start: 0.7977 (ptt) cc_final: 0.7648 (ppp) REVERT: C 131 MET cc_start: 0.9017 (tmm) cc_final: 0.8620 (tmm) REVERT: C 205 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.5450 (mtt) REVERT: D 12 LEU cc_start: 0.8972 (mm) cc_final: 0.8753 (mm) REVERT: E 88 LYS cc_start: 0.9039 (tppt) cc_final: 0.8753 (tppt) REVERT: E 92 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8633 (pttm) REVERT: G 29 ASP cc_start: 0.8095 (m-30) cc_final: 0.7500 (m-30) REVERT: G 42 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8796 (tm-30) REVERT: H 41 LEU cc_start: 0.6086 (mt) cc_final: 0.5486 (pp) REVERT: I 1 MET cc_start: 0.7667 (mmm) cc_final: 0.7212 (tpp) REVERT: I 145 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: I 183 MET cc_start: 0.7884 (tpt) cc_final: 0.7588 (tpt) REVERT: J 54 MET cc_start: 0.8765 (tpp) cc_final: 0.7825 (tpp) REVERT: J 119 ASP cc_start: 0.7387 (t0) cc_final: 0.6873 (t0) REVERT: J 135 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8402 (mm) REVERT: J 285 ASP cc_start: 0.7514 (p0) cc_final: 0.7163 (p0) REVERT: K 17 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7772 (t0) REVERT: K 54 MET cc_start: 0.8948 (tpp) cc_final: 0.8486 (tpp) REVERT: L 54 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7667 (mmp) REVERT: L 63 PHE cc_start: 0.8090 (t80) cc_final: 0.7749 (t80) REVERT: L 166 ASP cc_start: 0.6007 (t0) cc_final: 0.5298 (p0) REVERT: L 183 MET cc_start: 0.5631 (ttt) cc_final: 0.5271 (tpt) REVERT: L 283 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.5689 (m-80) REVERT: M 1 MET cc_start: 0.8015 (mmm) cc_final: 0.7462 (mtt) REVERT: M 19 GLN cc_start: 0.8011 (mp10) cc_final: 0.7324 (mp10) REVERT: M 194 TYR cc_start: 0.8422 (m-10) cc_final: 0.7807 (m-80) REVERT: M 261 PHE cc_start: 0.8565 (t80) cc_final: 0.8020 (t80) REVERT: M 318 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7365 (tm-30) REVERT: N 1 MET cc_start: 0.7475 (pmm) cc_final: 0.7243 (pmm) REVERT: N 59 HIS cc_start: 0.9490 (t-90) cc_final: 0.9246 (t-90) REVERT: N 162 HIS cc_start: 0.5253 (m170) cc_final: 0.4865 (m170) REVERT: N 202 LEU cc_start: 0.8445 (tp) cc_final: 0.8178 (tp) REVERT: N 334 LYS cc_start: 0.8099 (pttm) cc_final: 0.7571 (mmtm) REVERT: O 2 TYR cc_start: 0.8141 (m-80) cc_final: 0.7631 (m-80) REVERT: O 194 TYR cc_start: 0.8149 (m-80) cc_final: 0.7851 (m-80) REVERT: P 10 PHE cc_start: 0.8242 (p90) cc_final: 0.8021 (p90) REVERT: P 12 PHE cc_start: 0.8010 (m-80) cc_final: 0.7766 (m-80) REVERT: P 109 MET cc_start: 0.8370 (mmt) cc_final: 0.8045 (mtt) REVERT: P 172 PHE cc_start: 0.8568 (m-80) cc_final: 0.7544 (m-80) REVERT: A 36 LYS cc_start: 0.8819 (tptt) cc_final: 0.7596 (tptt) REVERT: A 48 THR cc_start: 0.6918 (OUTLIER) cc_final: 0.6520 (m) REVERT: A 107 LEU cc_start: 0.9351 (tp) cc_final: 0.9105 (pp) REVERT: A 118 LEU cc_start: 0.8458 (tp) cc_final: 0.8115 (tp) REVERT: A 140 LEU cc_start: 0.8686 (pp) cc_final: 0.8276 (mm) REVERT: A 177 MET cc_start: 0.6403 (mmt) cc_final: 0.5789 (mmt) REVERT: A 236 LEU cc_start: 0.6944 (mm) cc_final: 0.6518 (tp) REVERT: A 246 ASN cc_start: 0.8741 (m110) cc_final: 0.8430 (p0) REVERT: Q 2 SER cc_start: 0.4865 (m) cc_final: 0.4649 (p) REVERT: Q 27 ASN cc_start: 0.8719 (t0) cc_final: 0.8381 (t0) REVERT: Q 82 PHE cc_start: 0.6442 (t80) cc_final: 0.6101 (t80) REVERT: Q 99 MET cc_start: 0.7851 (ppp) cc_final: 0.7496 (ppp) REVERT: Q 161 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8043 (tmmt) REVERT: Q 169 LYS cc_start: 0.0555 (OUTLIER) cc_final: -0.1561 (ptmm) outliers start: 100 outliers final: 67 residues processed: 486 average time/residue: 0.1874 time to fit residues: 153.5507 Evaluate side-chains 465 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 388 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 23 VAL 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 139 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 16 VAL Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 92 LYS 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 G residue 70 SER Chi-restraints excluded: chain H residue 50 LEU 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 J residue 3 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 72 TYR 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 184 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 325 VAL Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 2 TYR Chi-restraints excluded: chain N residue 136 VAL 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 246 LEU 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 124 ILE Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 136 TYR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 THR 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 243 ASP Chi-restraints excluded: chain A residue 313 LEU 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 441 TYR Chi-restraints excluded: chain Q residue 111 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 62 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 389 optimal weight: 0.0040 chunk 347 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 298 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 368 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 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 106 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.090357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.075654 restraints weight = 160980.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.077885 restraints weight = 95134.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.079408 restraints weight = 64685.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.080477 restraints weight = 48253.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.081178 restraints weight = 38521.878| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35031 Z= 0.131 Angle : 0.681 14.293 47821 Z= 0.336 Chirality : 0.045 0.242 5505 Planarity : 0.004 0.056 5856 Dihedral : 11.863 179.811 5399 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.45 % Favored : 91.31 % Rotamer: Outliers : 2.80 % Allowed : 22.19 % Favored : 75.01 % 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: -2.27 (0.13), residues: 4144 helix: -0.65 (0.15), residues: 1313 sheet: -0.82 (0.22), residues: 560 loop : -2.28 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 180 TYR 0.031 0.001 TYR K 309 PHE 0.036 0.002 PHE A 56 TRP 0.016 0.001 TRP J 58 HIS 0.009 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (35025) covalent geometry : angle 0.68060 / 0.34 (47809) SS BOND : bond 0.00270 / 0.14 ( 6) SS BOND : angle 0.52642 / 0.32 ( 12) hydrogen bonds : bond 0.03391 / 2.24 ( 864) hydrogen bonds : angle 5.00578 / 3.50 ( 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 515 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 419 time to evaluate : 1.509 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: 0.8943 (OUTLIER) cc_final: 0.8672 (mm) REVERT: C 60 ASP cc_start: 0.8980 (m-30) cc_final: 0.8702 (m-30) REVERT: C 111 MET cc_start: 0.7988 (ptt) cc_final: 0.7629 (ppp) REVERT: C 131 MET cc_start: 0.9062 (tmm) cc_final: 0.8624 (tmm) REVERT: C 205 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5206 (mtt) REVERT: E 88 LYS cc_start: 0.9022 (tppt) cc_final: 0.8762 (tppt) REVERT: E 100 TRP cc_start: 0.7950 (m100) cc_final: 0.7680 (m100) REVERT: G 29 ASP cc_start: 0.8111 (m-30) cc_final: 0.7500 (m-30) REVERT: G 42 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8626 (tm-30) REVERT: G 46 LYS cc_start: 0.9463 (mtmt) cc_final: 0.9241 (mtmm) REVERT: G 56 LYS cc_start: 0.7539 (pttt) cc_final: 0.7206 (tttt) REVERT: H 29 ASP cc_start: 0.8540 (t70) cc_final: 0.8164 (p0) REVERT: H 41 LEU cc_start: 0.5827 (mt) cc_final: 0.5194 (pp) REVERT: I 1 MET cc_start: 0.7710 (mmm) cc_final: 0.7247 (tpp) REVERT: I 104 GLN cc_start: 0.8051 (tp40) cc_final: 0.7536 (tp40) REVERT: I 145 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: J 54 MET cc_start: 0.8652 (tpp) cc_final: 0.8112 (tpp) REVERT: J 119 ASP cc_start: 0.7438 (t0) cc_final: 0.6888 (t0) REVERT: J 135 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8372 (mm) REVERT: J 285 ASP cc_start: 0.7461 (p0) cc_final: 0.7130 (p0) REVERT: K 54 MET cc_start: 0.8953 (tpp) cc_final: 0.8716 (tpp) REVERT: L 54 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7505 (mmp) REVERT: L 63 PHE cc_start: 0.8066 (t80) cc_final: 0.7661 (t80) REVERT: L 166 ASP cc_start: 0.5960 (t0) cc_final: 0.5284 (p0) REVERT: L 183 MET cc_start: 0.5673 (ttt) cc_final: 0.5173 (tpt) REVERT: L 283 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.5644 (m-80) REVERT: M 1 MET cc_start: 0.8006 (mmm) cc_final: 0.7555 (mtt) REVERT: M 19 GLN cc_start: 0.7908 (mp10) cc_final: 0.7221 (mp10) REVERT: M 194 TYR cc_start: 0.8515 (m-10) cc_final: 0.7998 (m-80) REVERT: M 318 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7461 (tm-30) REVERT: N 1 MET cc_start: 0.7456 (pmm) cc_final: 0.7225 (pmm) REVERT: N 59 HIS cc_start: 0.9484 (t-90) cc_final: 0.9245 (t-90) REVERT: N 162 HIS cc_start: 0.5272 (m170) cc_final: 0.4842 (m170) REVERT: N 202 LEU cc_start: 0.8563 (tp) cc_final: 0.8281 (tp) REVERT: N 334 LYS cc_start: 0.8037 (pttm) cc_final: 0.7506 (mmtm) REVERT: O 2 TYR cc_start: 0.8126 (m-80) cc_final: 0.7600 (m-80) REVERT: O 194 TYR cc_start: 0.8288 (m-80) cc_final: 0.7970 (m-80) REVERT: P 12 PHE cc_start: 0.8072 (m-80) cc_final: 0.7806 (m-80) REVERT: P 42 LEU cc_start: 0.8813 (mm) cc_final: 0.8607 (mp) REVERT: P 109 MET cc_start: 0.8337 (mmt) cc_final: 0.8093 (mtt) REVERT: P 141 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7357 (mpp) REVERT: P 172 PHE cc_start: 0.8572 (m-80) cc_final: 0.7637 (m-80) REVERT: A 36 LYS cc_start: 0.8812 (tptt) cc_final: 0.7565 (tptt) REVERT: A 48 THR cc_start: 0.7056 (OUTLIER) cc_final: 0.6657 (m) REVERT: A 107 LEU cc_start: 0.9350 (tp) cc_final: 0.9102 (pp) REVERT: A 118 LEU cc_start: 0.8478 (tp) cc_final: 0.8130 (tp) REVERT: A 140 LEU cc_start: 0.8642 (pp) cc_final: 0.8228 (mm) REVERT: A 177 MET cc_start: 0.6379 (mmt) cc_final: 0.5768 (mmt) REVERT: A 236 LEU cc_start: 0.6959 (mm) cc_final: 0.6537 (tp) REVERT: A 246 ASN cc_start: 0.8752 (m110) cc_final: 0.8459 (p0) REVERT: Q 2 SER cc_start: 0.4924 (m) cc_final: 0.4699 (p) REVERT: Q 27 ASN cc_start: 0.8704 (t0) cc_final: 0.8362 (t0) REVERT: Q 82 PHE cc_start: 0.6527 (t80) cc_final: 0.6165 (t80) REVERT: Q 99 MET cc_start: 0.7854 (ppp) cc_final: 0.7555 (ppp) REVERT: Q 161 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8078 (tmmt) REVERT: Q 169 LYS cc_start: 0.0467 (OUTLIER) cc_final: -0.1665 (ptmm) outliers start: 96 outliers final: 74 residues processed: 482 average time/residue: 0.2199 time to fit residues: 176.6863 Evaluate side-chains 471 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 388 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 23 VAL 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 139 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 16 VAL Chi-restraints excluded: chain D residue 99 LEU 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 G residue 27 VAL Chi-restraints excluded: chain H residue 50 LEU 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 3 VAL Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 72 TYR 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 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 269 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 328 LEU 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 5 ILE 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 328 LEU Chi-restraints excluded: chain P residue 20 TYR 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 136 TYR Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 THR 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 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 111 LEU 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: 10.0000 chunk 359 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 316 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 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** Q 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.087514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.072684 restraints weight = 161584.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.074879 restraints weight = 95485.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.076382 restraints weight = 64762.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.077428 restraints weight = 48261.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.078165 restraints weight = 38550.935| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 35031 Z= 0.169 Angle : 0.708 14.363 47821 Z= 0.352 Chirality : 0.046 0.453 5505 Planarity : 0.004 0.060 5856 Dihedral : 11.910 179.259 5399 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.88 % Favored : 90.83 % Rotamer: Outliers : 2.92 % Allowed : 22.16 % Favored : 74.93 % 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: -2.17 (0.13), residues: 4144 helix: -0.51 (0.15), residues: 1288 sheet: -0.91 (0.22), residues: 578 loop : -2.20 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 180 TYR 0.031 0.002 TYR G 45 PHE 0.041 0.002 PHE P 89 TRP 0.020 0.002 TRP J 58 HIS 0.012 0.002 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (35025) covalent geometry : angle 0.70764 / 0.35 (47809) SS BOND : bond 0.00265 / 0.14 ( 6) SS BOND : angle 0.59767 / 0.36 ( 12) hydrogen bonds : bond 0.03537 / 2.34 ( 864) hydrogen bonds : angle 5.09803 / 3.58 ( 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 501 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 401 time to evaluate : 1.253 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: 0.7805 (ptt) cc_final: 0.7477 (ppp) REVERT: C 131 MET cc_start: 0.9042 (tmm) cc_final: 0.8613 (tmm) REVERT: C 205 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5474 (mtt) REVERT: D 106 ASN cc_start: 0.8450 (m-40) cc_final: 0.7949 (p0) REVERT: E 88 LYS cc_start: 0.9023 (tppt) cc_final: 0.8762 (tppt) REVERT: F 72 GLU cc_start: 0.8476 (tp30) cc_final: 0.8120 (tp30) REVERT: G 21 GLU cc_start: 0.6888 (mp0) cc_final: 0.6466 (mp0) REVERT: G 29 ASP cc_start: 0.8089 (m-30) cc_final: 0.7425 (m-30) REVERT: G 42 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8683 (tm-30) REVERT: H 41 LEU cc_start: 0.5969 (mt) cc_final: 0.5303 (pp) REVERT: I 1 MET cc_start: 0.7675 (mmm) cc_final: 0.7282 (tpp) REVERT: I 31 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7791 (mmtp) REVERT: I 104 GLN cc_start: 0.8160 (tp40) cc_final: 0.7663 (tp40) REVERT: I 145 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: J 54 MET cc_start: 0.8786 (tpp) cc_final: 0.8528 (mmm) REVERT: J 119 ASP cc_start: 0.7628 (t0) cc_final: 0.6974 (t0) REVERT: J 285 ASP cc_start: 0.7479 (p0) cc_final: 0.7127 (p0) REVERT: K 54 MET cc_start: 0.9059 (tpp) cc_final: 0.8808 (tpp) REVERT: L 54 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7948 (mmp) REVERT: L 63 PHE cc_start: 0.8273 (t80) cc_final: 0.7895 (t80) REVERT: L 166 ASP cc_start: 0.6139 (t0) cc_final: 0.5396 (p0) REVERT: L 183 MET cc_start: 0.5875 (ttt) cc_final: 0.5413 (tpt) REVERT: L 283 TYR cc_start: 0.6213 (OUTLIER) cc_final: 0.5379 (m-80) REVERT: M 1 MET cc_start: 0.8177 (mmm) cc_final: 0.7679 (mtt) REVERT: M 194 TYR cc_start: 0.8609 (m-10) cc_final: 0.8016 (m-80) REVERT: M 318 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7457 (tm-30) REVERT: N 59 HIS cc_start: 0.9493 (t-90) cc_final: 0.9281 (t-90) REVERT: N 334 LYS cc_start: 0.8155 (pttm) cc_final: 0.7648 (mmtm) REVERT: O 194 TYR cc_start: 0.8518 (m-80) cc_final: 0.8227 (m-80) REVERT: P 109 MET cc_start: 0.8446 (mmt) cc_final: 0.8206 (mtt) REVERT: P 172 PHE cc_start: 0.8724 (m-80) cc_final: 0.7693 (m-80) REVERT: A 36 LYS cc_start: 0.8949 (tptt) cc_final: 0.7857 (tptt) REVERT: A 48 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6735 (m) REVERT: A 107 LEU cc_start: 0.9370 (tp) cc_final: 0.9119 (pp) REVERT: A 118 LEU cc_start: 0.8374 (tp) cc_final: 0.8043 (tp) REVERT: A 140 LEU cc_start: 0.8688 (pp) cc_final: 0.8282 (mm) REVERT: A 159 GLN cc_start: 0.8807 (pm20) cc_final: 0.8513 (pm20) REVERT: A 177 MET cc_start: 0.6422 (mmt) cc_final: 0.5958 (mmm) REVERT: A 236 LEU cc_start: 0.7357 (mm) cc_final: 0.7050 (tp) REVERT: Q 2 SER cc_start: 0.5127 (m) cc_final: 0.4859 (p) REVERT: Q 27 ASN cc_start: 0.8733 (t0) cc_final: 0.8420 (t0) REVERT: Q 115 MET cc_start: 0.8687 (mmp) cc_final: 0.8379 (mmt) REVERT: Q 161 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8093 (tmmt) REVERT: Q 169 LYS cc_start: 0.0912 (OUTLIER) cc_final: -0.1180 (ptmm) REVERT: Q 213 TYR cc_start: 0.7095 (t80) cc_final: 0.6637 (t80) outliers start: 100 outliers final: 85 residues processed: 465 average time/residue: 0.2148 time to fit residues: 166.4943 Evaluate side-chains 471 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 380 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 42 SER 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 139 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 16 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 50 LEU 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 G residue 27 VAL Chi-restraints excluded: chain G residue 97 LEU 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 30 THR Chi-restraints excluded: chain I residue 145 GLU 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 16 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 51 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 L residue 44 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 54 MET 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 19 GLN 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 260 VAL 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 M residue 325 VAL Chi-restraints excluded: chain M residue 328 LEU 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 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 154 THR Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 THR 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 228 SER 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 A residue 501 ILE Chi-restraints excluded: chain Q residue 111 LEU 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: 1.9990 chunk 199 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 410 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 412 optimal weight: 4.9990 chunk 186 optimal weight: 0.4980 chunk 135 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN ** K 90 GLN ** 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.088962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.074168 restraints weight = 160952.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.076410 restraints weight = 94601.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.077928 restraints weight = 63918.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.078982 restraints weight = 47556.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.079736 restraints weight = 37945.378| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35031 Z= 0.133 Angle : 0.709 14.837 47821 Z= 0.345 Chirality : 0.046 0.321 5505 Planarity : 0.004 0.050 5856 Dihedral : 11.927 179.635 5399 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.42 % Favored : 91.34 % Rotamer: Outliers : 2.62 % Allowed : 22.77 % Favored : 74.61 % 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: -2.22 (0.13), residues: 4144 helix: -0.59 (0.15), residues: 1320 sheet: -0.86 (0.22), residues: 573 loop : -2.25 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 91 TYR 0.035 0.002 TYR F 11 PHE 0.033 0.002 PHE A 56 TRP 0.014 0.001 TRP J 58 HIS 0.013 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (35025) covalent geometry : angle 0.70874 / 0.35 (47809) SS BOND : bond 0.00265 / 0.13 ( 6) SS BOND : angle 0.49769 / 0.30 ( 12) hydrogen bonds : bond 0.03294 / 2.19 ( 864) hydrogen bonds : angle 5.05158 / 3.55 ( 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 498 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 408 time to evaluate : 1.359 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: C 58 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8674 (mm) REVERT: C 111 MET cc_start: 0.7809 (ptt) cc_final: 0.7459 (ppp) REVERT: C 131 MET cc_start: 0.9057 (tmm) cc_final: 0.8609 (tmm) REVERT: C 205 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.5240 (mtt) REVERT: D 106 ASN cc_start: 0.8357 (m-40) cc_final: 0.7851 (p0) REVERT: F 72 GLU cc_start: 0.8484 (tp30) cc_final: 0.8129 (tp30) REVERT: G 29 ASP cc_start: 0.8070 (m-30) cc_final: 0.7427 (m-30) REVERT: G 42 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8647 (tm-30) REVERT: G 46 LYS cc_start: 0.9333 (mtmt) cc_final: 0.9093 (mtmm) REVERT: H 41 LEU cc_start: 0.5996 (mt) cc_final: 0.5315 (pp) REVERT: I 1 MET cc_start: 0.7667 (mmm) cc_final: 0.7338 (tpp) REVERT: I 31 LYS cc_start: 0.7989 (mmtp) cc_final: 0.7688 (mmtp) REVERT: I 104 GLN cc_start: 0.8145 (tp40) cc_final: 0.7637 (tp40) REVERT: I 145 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: I 183 MET cc_start: 0.8037 (tpt) cc_final: 0.7632 (tpt) REVERT: J 54 MET cc_start: 0.8643 (tpp) cc_final: 0.7979 (tpp) REVERT: J 107 ASP cc_start: 0.7602 (t0) cc_final: 0.7396 (t70) REVERT: J 119 ASP cc_start: 0.7574 (t0) cc_final: 0.6936 (t0) REVERT: J 135 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8363 (mm) REVERT: J 232 LYS cc_start: 0.8585 (tttt) cc_final: 0.8106 (tptt) REVERT: J 285 ASP cc_start: 0.7450 (p0) cc_final: 0.7145 (p0) REVERT: K 17 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7800 (t0) REVERT: K 54 MET cc_start: 0.8991 (tpp) cc_final: 0.8737 (tpp) REVERT: L 54 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7720 (mmp) REVERT: L 63 PHE cc_start: 0.8229 (t80) cc_final: 0.7855 (t80) REVERT: L 166 ASP cc_start: 0.6049 (t0) cc_final: 0.5335 (p0) REVERT: L 183 MET cc_start: 0.5785 (ttt) cc_final: 0.5318 (tpt) REVERT: L 283 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: M 1 MET cc_start: 0.8039 (mmm) cc_final: 0.7606 (mtt) REVERT: M 318 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7457 (tm-30) REVERT: N 160 ILE cc_start: 0.9027 (pt) cc_final: 0.8758 (mp) REVERT: N 334 LYS cc_start: 0.8143 (pttm) cc_final: 0.7655 (mmtm) REVERT: P 12 PHE cc_start: 0.8547 (m-80) cc_final: 0.8026 (m-10) REVERT: P 172 PHE cc_start: 0.8717 (m-80) cc_final: 0.7738 (m-80) REVERT: A 36 LYS cc_start: 0.8966 (tptt) cc_final: 0.7814 (tptt) REVERT: A 48 THR cc_start: 0.7200 (OUTLIER) cc_final: 0.6822 (m) REVERT: A 107 LEU cc_start: 0.9366 (tp) cc_final: 0.9106 (pp) REVERT: A 118 LEU cc_start: 0.8351 (tp) cc_final: 0.8009 (tp) REVERT: A 140 LEU cc_start: 0.8674 (pp) cc_final: 0.8044 (mm) REVERT: A 159 GLN cc_start: 0.8765 (pm20) cc_final: 0.8512 (pm20) REVERT: A 177 MET cc_start: 0.6394 (mmt) cc_final: 0.5788 (mmt) REVERT: A 246 ASN cc_start: 0.8721 (m110) cc_final: 0.8497 (p0) REVERT: Q 2 SER cc_start: 0.5164 (m) cc_final: 0.4886 (p) REVERT: Q 27 ASN cc_start: 0.8778 (t0) cc_final: 0.8461 (t0) REVERT: Q 50 ASP cc_start: 0.8192 (m-30) cc_final: 0.7780 (t0) REVERT: Q 115 MET cc_start: 0.8673 (mmp) cc_final: 0.8386 (mmt) REVERT: Q 161 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8089 (tmmt) REVERT: Q 169 LYS cc_start: 0.0594 (OUTLIER) cc_final: -0.1362 (ptmm) outliers start: 90 outliers final: 71 residues processed: 466 average time/residue: 0.2088 time to fit residues: 163.9384 Evaluate side-chains 464 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 384 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 23 VAL 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 139 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 16 VAL Chi-restraints excluded: chain D residue 99 LEU 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 G residue 27 VAL Chi-restraints excluded: chain G residue 97 LEU 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 30 THR Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 17 ASN 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 L residue 54 MET 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 19 GLN 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 269 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 328 LEU 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 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 154 THR Chi-restraints excluded: chain P residue 179 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 THR 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 228 SER 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 A residue 501 ILE Chi-restraints excluded: chain Q residue 149 MET Chi-restraints excluded: chain Q residue 169 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 248 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 chunk 337 optimal weight: 20.0000 chunk 311 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 410 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 chunk 316 optimal weight: 0.0030 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN ** K 90 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.089066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.074307 restraints weight = 160357.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.076524 restraints weight = 94419.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.078041 restraints weight = 63901.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.079090 restraints weight = 47537.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.079823 restraints weight = 37966.610| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35031 Z= 0.133 Angle : 0.715 14.977 47821 Z= 0.347 Chirality : 0.046 0.315 5505 Planarity : 0.004 0.064 5856 Dihedral : 11.919 179.334 5399 Min Nonbonded Distance : 1.162 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.54 % Favored : 91.22 % Rotamer: Outliers : 2.54 % Allowed : 23.15 % Favored : 74.31 % 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: -2.22 (0.13), residues: 4144 helix: -0.58 (0.15), residues: 1311 sheet: -0.99 (0.22), residues: 593 loop : -2.22 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 49 TYR 0.044 0.002 TYR G 45 PHE 0.034 0.002 PHE A 56 TRP 0.016 0.001 TRP E 100 HIS 0.012 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (35025) covalent geometry : angle 0.71480 / 0.35 (47809) SS BOND : bond 0.00243 / 0.12 ( 6) SS BOND : angle 0.47859 / 0.28 ( 12) hydrogen bonds : bond 0.03302 / 2.20 ( 864) hydrogen bonds : angle 5.06342 / 3.56 ( 2380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6487.49 seconds wall clock time: 113 minutes 32.68 seconds (6812.68 seconds total)