Starting phenix.real_space_refine on Sun Jun 29 13:10:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tr9_26083/06_2025/7tr9_26083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr9_26083/06_2025/7tr9_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_26083/06_2025/7tr9_26083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr9_26083/06_2025/7tr9_26083.map" model { file = "/net/cci-nas-00/data/ceres_data/7tr9_26083/06_2025/7tr9_26083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr9_26083/06_2025/7tr9_26083.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'TYR:plan': 1, 'GLU: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: 19.24, per 1000 atoms: 0.56 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: 8.29 Conformation dependent library (CDL) restraints added in 4.1 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: 10.74 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: 10.35 Time building geometry restraints manager: 9.78 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=" 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 bond pdb=" C3' U R 11 " pdb=" O3' U R 11 " ideal model delta sigma weight residual 1.417 1.468 -0.051 1.50e-02 4.44e+03 1.14e+01 ... (remaining 35020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 46911 2.28 - 4.57: 778 4.57 - 6.85: 106 6.85 - 9.14: 10 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: 20707 35.88 - 71.75: 381 71.75 - 107.63: 28 107.63 - 143.50: 0 143.50 - 179.38: 5 Dihedral angle restraints: 21121 sinusoidal: 8984 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 21118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4950 0.077 - 0.154: 521 0.154 - 0.231: 26 0.231 - 0.307: 6 0.307 - 0.384: 2 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=" 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 chirality pdb=" CA THR J 51 " pdb=" N THR J 51 " pdb=" C THR J 51 " pdb=" CB THR J 51 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5502 not shown) Planarity restraints: 5856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT S 46 " 0.058 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" N1 DT S 46 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DT S 46 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT S 46 " -0.040 2.00e-02 2.50e+03 pdb=" N3 DT S 46 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT S 46 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT S 46 " 0.053 2.00e-02 2.50e+03 pdb=" C5 DT S 46 " -0.006 2.00e-02 2.50e+03 pdb=" C7 DT S 46 " -0.035 2.00e-02 2.50e+03 pdb=" C6 DT S 46 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 181 " -0.024 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ALA J 181 " 0.079 2.00e-02 2.50e+03 pdb=" O ALA J 181 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN J 182 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 130 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ARG L 130 " -0.078 2.00e-02 2.50e+03 pdb=" O ARG L 130 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG L 131 " 0.026 2.00e-02 2.50e+03 ... (remaining 5853 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.79: 8501 2.79 - 3.49: 50398 3.49 - 4.20: 86084 4.20 - 4.90: 144475 Nonbonded interactions: 289461 Sorted by model distance: nonbonded pdb="NI NI Q 301 " pdb="NI NI Q 302 " model vdw 1.387 1.320 nonbonded pdb=" NZ LYS C 136 " pdb=" N7 DG S 61 " model vdw 1.635 3.200 nonbonded pdb=" OD2 ASP Q 61 " pdb="NI NI Q 301 " model vdw 2.039 2.180 nonbonded pdb=" OD2 ASP Q 61 " pdb="NI NI Q 302 " model vdw 2.090 2.180 nonbonded pdb=" NH1 ARG P 95 " pdb=" OP1 DG S 60 " model vdw 2.117 3.120 ... (remaining 289456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 3 through 109) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 164 or resid 180 th \ rough 335)) selection = (chain 'J' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 164 or resid 180 through 335)) selection = (chain 'K' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'L' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'M' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'N' and resid 1 through 335) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 77.280 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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= 0.177 Angle : 0.676 11.423 47821 Z= 0.383 Chirality : 0.047 0.384 5505 Planarity : 0.004 0.047 5856 Dihedral : 13.729 179.379 13295 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 16.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.001 TRP G 4 HIS 0.007 0.001 HIS I 162 PHE 0.020 0.001 PHE J 60 TYR 0.032 0.001 TYR P 20 ARG 0.006 0.000 ARG L 132 Details of bonding type rmsd hydrogen bonds : bond 0.19597 ( 864) hydrogen bonds : angle 7.11850 ( 2380) SS BOND : bond 0.00027 ( 6) SS BOND : angle 0.20403 ( 12) covalent geometry : bond 0.00306 (35025) covalent geometry : angle 0.67636 (47809) *********************** 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 : 3.636 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: 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: 0.8423 (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: 0.8113 (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: 0.7901 (m-30) REVERT: G 42 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8748 (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: 0.7660 (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: 0.7078 (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: 0.8425 (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: 0.7466 (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: 0.5779 (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: 0.6598 (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: 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: 0.7702 (pp20) REVERT: M 63 PHE cc_start: 0.7923 (t80) cc_final: 0.7312 (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: 0.6623 (mp) REVERT: M 207 ILE cc_start: 0.7091 (mt) cc_final: 0.6828 (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: 0.8151 (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: 0.7634 (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: 0.4868 (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: 0.6471 (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 78 LEU cc_start: 0.8128 (mt) cc_final: 0.7923 (mt) 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: 0.7454 (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: 0.8568 (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: 0.5018 time to fit residues: 706.1162 Evaluate side-chains 531 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 529 time to evaluate : 3.408 ------------------------------------------------------------------------------- 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 352 optimal weight: 9.9990 chunk 316 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 213 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 326 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 243 optimal weight: 0.4980 chunk 378 optimal weight: 0.0870 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN E 7 ASN ** I 59 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 J 104 GLN J 182 GLN J 229 ASN K 25 ASN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 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 90 GLN ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.103061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.088812 restraints weight = 161737.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.091244 restraints weight = 99490.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.092950 restraints weight = 68303.922| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35031 Z= 0.148 Angle : 0.680 12.244 47821 Z= 0.343 Chirality : 0.045 0.231 5505 Planarity : 0.005 0.050 5856 Dihedral : 13.336 178.725 5550 Min Nonbonded Distance : 1.359 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.47 % Favored : 91.22 % Rotamer: Outliers : 1.92 % Allowed : 13.12 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.13), residues: 4144 helix: -0.93 (0.15), residues: 1254 sheet: -0.69 (0.22), residues: 545 loop : -2.42 (0.12), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 4 HIS 0.009 0.001 HIS L 59 PHE 0.032 0.002 PHE I 282 TYR 0.024 0.002 TYR A 408 ARG 0.007 0.001 ARG K 10 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 864) hydrogen bonds : angle 5.33848 ( 2380) SS BOND : bond 0.00833 ( 6) SS BOND : angle 0.93465 ( 12) covalent geometry : bond 0.00320 (35025) covalent geometry : angle 0.67993 (47809) *********************** 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 648 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 582 time to evaluate : 3.503 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: C 60 ASP cc_start: 0.8879 (m-30) cc_final: 0.8666 (m-30) REVERT: C 157 TYR cc_start: 0.9019 (t80) cc_final: 0.8643 (t80) REVERT: C 177 ASP cc_start: 0.8662 (p0) cc_final: 0.7701 (t70) REVERT: C 205 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5073 (mtt) REVERT: C 276 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8425 (ttmt) REVERT: D 35 ARG cc_start: 0.6705 (ptp90) cc_final: 0.6077 (mtt90) REVERT: D 48 LEU cc_start: 0.7962 (tp) cc_final: 0.7728 (tp) REVERT: G 29 ASP cc_start: 0.8164 (m-30) cc_final: 0.7570 (m-30) REVERT: G 42 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8838 (tm-30) REVERT: G 72 GLU cc_start: 0.8062 (pm20) cc_final: 0.7745 (pm20) REVERT: H 25 TYR cc_start: 0.7683 (m-10) cc_final: 0.7210 (m-10) REVERT: I 141 ILE cc_start: 0.9086 (mm) cc_final: 0.8788 (mm) REVERT: I 306 VAL cc_start: 0.8646 (t) cc_final: 0.8241 (p) REVERT: J 107 ASP cc_start: 0.7147 (t70) cc_final: 0.6875 (t70) REVERT: J 119 ASP cc_start: 0.7337 (t0) cc_final: 0.6811 (t0) REVERT: J 213 VAL cc_start: 0.7516 (m) cc_final: 0.7280 (m) REVERT: J 232 LYS cc_start: 0.8353 (tttt) cc_final: 0.7702 (tptt) REVERT: J 245 MET cc_start: 0.8899 (mmp) cc_final: 0.8671 (mmt) REVERT: J 285 ASP cc_start: 0.7389 (p0) cc_final: 0.7005 (p0) REVERT: K 54 MET cc_start: 0.8740 (tpt) cc_final: 0.8485 (tpp) REVERT: K 218 ASN cc_start: 0.8238 (m-40) cc_final: 0.7973 (m-40) REVERT: L 63 PHE cc_start: 0.7102 (t80) cc_final: 0.6722 (t80) REVERT: L 166 ASP cc_start: 0.5916 (t0) cc_final: 0.5667 (p0) REVERT: L 196 PHE cc_start: 0.7526 (p90) cc_final: 0.7197 (p90) REVERT: L 207 ILE cc_start: 0.7449 (mm) cc_final: 0.7217 (mm) REVERT: M 19 GLN cc_start: 0.8128 (mp10) cc_final: 0.7576 (mp10) REVERT: M 63 PHE cc_start: 0.7832 (t80) cc_final: 0.6726 (t80) REVERT: M 67 PHE cc_start: 0.8317 (t80) cc_final: 0.7999 (m-80) REVERT: M 135 LEU cc_start: 0.6979 (mp) cc_final: 0.6741 (mp) REVERT: M 211 LEU cc_start: 0.8749 (mt) cc_final: 0.8519 (tt) REVERT: M 250 ILE cc_start: 0.8212 (mp) cc_final: 0.7819 (mp) REVERT: M 261 PHE cc_start: 0.8084 (t80) cc_final: 0.7497 (t80) REVERT: M 269 ILE cc_start: 0.7327 (mp) cc_final: 0.7077 (tt) REVERT: N 59 HIS cc_start: 0.9338 (t-90) cc_final: 0.8728 (t-90) REVERT: N 65 ASP cc_start: 0.8893 (m-30) cc_final: 0.8613 (m-30) REVERT: N 147 PHE cc_start: 0.8118 (t80) cc_final: 0.7846 (t80) REVERT: N 162 HIS cc_start: 0.5357 (m170) cc_final: 0.5071 (m170) REVERT: N 237 SER cc_start: 0.9151 (t) cc_final: 0.8936 (p) REVERT: N 258 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6504 (t80) REVERT: N 333 VAL cc_start: 0.8381 (t) cc_final: 0.7764 (m) REVERT: N 334 LYS cc_start: 0.8108 (pttt) cc_final: 0.7702 (mmtt) REVERT: O 194 TYR cc_start: 0.6665 (m-80) cc_final: 0.6269 (m-80) REVERT: P 10 PHE cc_start: 0.8077 (p90) cc_final: 0.7830 (p90) REVERT: P 13 PHE cc_start: 0.6840 (m-80) cc_final: 0.6464 (m-80) REVERT: P 20 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: P 137 LEU cc_start: 0.8376 (mt) cc_final: 0.8150 (pp) REVERT: P 141 MET cc_start: 0.7294 (tpp) cc_final: 0.6997 (mmt) REVERT: P 172 PHE cc_start: 0.7709 (m-80) cc_final: 0.7094 (m-80) REVERT: P 218 TYR cc_start: 0.9013 (t80) cc_final: 0.8770 (t80) REVERT: A 33 ASN cc_start: 0.7471 (t0) cc_final: 0.7209 (t0) REVERT: A 107 LEU cc_start: 0.9370 (tp) cc_final: 0.9089 (pp) REVERT: A 118 LEU cc_start: 0.8333 (tp) cc_final: 0.7937 (tp) REVERT: A 133 TRP cc_start: 0.8442 (t60) cc_final: 0.8149 (t60) REVERT: A 177 MET cc_start: 0.6319 (mmt) cc_final: 0.6077 (mmt) REVERT: A 198 MET cc_start: 0.7583 (ptp) cc_final: 0.7296 (tpp) REVERT: A 246 ASN cc_start: 0.8462 (m110) cc_final: 0.8128 (p0) REVERT: A 340 ASP cc_start: 0.8595 (t0) cc_final: 0.8197 (m-30) REVERT: Q 16 GLU cc_start: 0.8654 (mp0) cc_final: 0.8106 (mp0) REVERT: Q 27 ASN cc_start: 0.8722 (t0) cc_final: 0.8263 (t0) REVERT: Q 50 ASP cc_start: 0.8246 (m-30) cc_final: 0.7899 (m-30) REVERT: Q 213 TYR cc_start: 0.6668 (t80) cc_final: 0.6289 (t80) outliers start: 66 outliers final: 41 residues processed: 619 average time/residue: 0.4695 time to fit residues: 469.8187 Evaluate side-chains 526 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 482 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain E residue 53 LYS 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 242 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 168 ASP 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 201 ASP Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 246 LEU 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 227 ASP Chi-restraints excluded: chain O residue 307 PHE 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 130 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 372 optimal weight: 20.0000 chunk 413 optimal weight: 9.9990 chunk 390 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 286 optimal weight: 0.0570 chunk 412 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 overall best weight: 2.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 GLN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 59 HIS L 229 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 GLN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 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 A 263 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.096024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.081348 restraints weight = 163592.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.083665 restraints weight = 99262.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.085297 restraints weight = 67936.634| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 35031 Z= 0.201 Angle : 0.682 10.878 47821 Z= 0.349 Chirality : 0.046 0.326 5505 Planarity : 0.005 0.059 5856 Dihedral : 13.329 178.900 5545 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.88 % Favored : 90.83 % Rotamer: Outliers : 2.77 % Allowed : 16.24 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.13), residues: 4144 helix: -0.78 (0.15), residues: 1262 sheet: -0.78 (0.22), residues: 574 loop : -2.36 (0.12), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 58 HIS 0.011 0.002 HIS K 14 PHE 0.035 0.002 PHE A 56 TYR 0.030 0.002 TYR G 45 ARG 0.025 0.001 ARG J 221 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 864) hydrogen bonds : angle 5.16187 ( 2380) SS BOND : bond 0.00457 ( 6) SS BOND : angle 0.85252 ( 12) covalent geometry : bond 0.00447 (35025) covalent geometry : angle 0.68208 (47809) *********************** 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 604 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 509 time to evaluate : 3.685 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 60 ASP cc_start: 0.9005 (m-30) cc_final: 0.8724 (m-30) REVERT: C 131 MET cc_start: 0.8715 (tmm) cc_final: 0.8374 (tmm) REVERT: C 177 ASP cc_start: 0.8839 (p0) cc_final: 0.7969 (t70) REVERT: C 185 GLN cc_start: 0.8010 (pm20) cc_final: 0.7232 (pp30) REVERT: C 205 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.5499 (mtt) REVERT: C 308 MET cc_start: 0.7667 (mpp) cc_final: 0.7124 (mpp) REVERT: C 312 LEU cc_start: 0.9066 (tp) cc_final: 0.8830 (tp) REVERT: D 48 LEU cc_start: 0.8441 (tp) cc_final: 0.8103 (tp) REVERT: D 89 ASP cc_start: 0.7237 (t0) cc_final: 0.6867 (p0) REVERT: E 46 LYS cc_start: 0.9360 (mmmm) cc_final: 0.9002 (mmmm) REVERT: E 86 ASN cc_start: 0.7584 (p0) cc_final: 0.6994 (t0) REVERT: E 88 LYS cc_start: 0.9149 (tptt) cc_final: 0.8089 (pttt) REVERT: E 89 ASP cc_start: 0.8307 (p0) cc_final: 0.7776 (p0) REVERT: G 29 ASP cc_start: 0.8062 (m-30) cc_final: 0.7536 (m-30) REVERT: G 42 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8754 (tm-30) REVERT: G 72 GLU cc_start: 0.8072 (pm20) cc_final: 0.7824 (pm20) REVERT: H 25 TYR cc_start: 0.7594 (m-10) cc_final: 0.7137 (m-10) REVERT: H 41 LEU cc_start: 0.5890 (mt) cc_final: 0.5450 (pp) REVERT: I 1 MET cc_start: 0.7503 (mmm) cc_final: 0.6784 (tpp) REVERT: I 306 VAL cc_start: 0.9087 (t) cc_final: 0.8819 (p) REVERT: J 107 ASP cc_start: 0.7550 (t70) cc_final: 0.7321 (t70) REVERT: J 119 ASP cc_start: 0.7562 (t0) cc_final: 0.7082 (t0) REVERT: J 213 VAL cc_start: 0.8119 (m) cc_final: 0.7889 (m) REVERT: J 227 ASP cc_start: 0.8428 (t70) cc_final: 0.8226 (t0) REVERT: J 232 LYS cc_start: 0.8545 (tttt) cc_final: 0.7958 (tptt) REVERT: J 285 ASP cc_start: 0.7521 (p0) cc_final: 0.7222 (p0) REVERT: K 54 MET cc_start: 0.8975 (tpt) cc_final: 0.8629 (tpp) REVERT: K 111 ILE cc_start: 0.8508 (mt) cc_final: 0.8263 (mt) REVERT: K 218 ASN cc_start: 0.8221 (m-40) cc_final: 0.7895 (m-40) REVERT: L 63 PHE cc_start: 0.7391 (t80) cc_final: 0.7021 (t80) REVERT: L 166 ASP cc_start: 0.6000 (t0) cc_final: 0.5612 (p0) REVERT: L 207 ILE cc_start: 0.7934 (mm) cc_final: 0.7594 (mm) REVERT: M 1 MET cc_start: 0.7596 (mmm) cc_final: 0.6557 (mtt) REVERT: M 60 PHE cc_start: 0.7242 (t80) cc_final: 0.6752 (t80) REVERT: M 63 PHE cc_start: 0.7950 (t80) cc_final: 0.7689 (t80) REVERT: M 135 LEU cc_start: 0.7784 (mp) cc_final: 0.7509 (mp) REVERT: M 211 LEU cc_start: 0.8831 (mt) cc_final: 0.8577 (tt) REVERT: M 250 ILE cc_start: 0.8226 (mp) cc_final: 0.7865 (mp) REVERT: M 261 PHE cc_start: 0.8509 (t80) cc_final: 0.8271 (t80) REVERT: M 318 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7741 (tm-30) REVERT: N 2 TYR cc_start: 0.7349 (m-80) cc_final: 0.7105 (m-80) REVERT: N 59 HIS cc_start: 0.9405 (t-90) cc_final: 0.8767 (t-90) REVERT: N 78 GLU cc_start: 0.8935 (mp0) cc_final: 0.8646 (pm20) REVERT: N 258 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.6634 (t80) REVERT: O 31 LYS cc_start: 0.7785 (mppt) cc_final: 0.7077 (mtmt) REVERT: O 194 TYR cc_start: 0.6847 (m-80) cc_final: 0.6388 (m-80) REVERT: P 10 PHE cc_start: 0.8333 (p90) cc_final: 0.8027 (p90) REVERT: P 12 PHE cc_start: 0.8042 (m-10) cc_final: 0.7783 (m-80) REVERT: P 20 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: P 85 ILE cc_start: 0.8736 (tt) cc_final: 0.8473 (tp) REVERT: P 89 PHE cc_start: 0.8187 (m-10) cc_final: 0.7907 (m-10) REVERT: P 172 PHE cc_start: 0.7953 (m-80) cc_final: 0.7328 (m-80) REVERT: A 56 PHE cc_start: 0.7534 (m-10) cc_final: 0.7061 (t80) REVERT: A 107 LEU cc_start: 0.9304 (tp) cc_final: 0.9074 (pp) REVERT: A 118 LEU cc_start: 0.8449 (tp) cc_final: 0.8141 (tp) REVERT: A 140 LEU cc_start: 0.8499 (pp) cc_final: 0.7988 (mm) REVERT: A 177 MET cc_start: 0.6364 (mmt) cc_final: 0.6115 (mmm) REVERT: A 246 ASN cc_start: 0.8712 (m110) cc_final: 0.8314 (p0) REVERT: Q 16 GLU cc_start: 0.8682 (mp0) cc_final: 0.8152 (mp0) REVERT: Q 27 ASN cc_start: 0.8552 (t0) cc_final: 0.8203 (t0) REVERT: Q 50 ASP cc_start: 0.8269 (m-30) cc_final: 0.7902 (m-30) REVERT: Q 115 MET cc_start: 0.8859 (mmp) cc_final: 0.8465 (mmm) REVERT: Q 161 LYS cc_start: 0.8388 (mmtm) cc_final: 0.7876 (tmmt) outliers start: 95 outliers final: 56 residues processed: 567 average time/residue: 0.4874 time to fit residues: 456.0593 Evaluate side-chains 493 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 434 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 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 12 LEU Chi-restraints excluded: chain E residue 45 TYR Chi-restraints excluded: chain E residue 50 LEU 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 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 5 ILE Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 266 LEU 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 257 SER 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 127 LYS Chi-restraints excluded: chain O residue 133 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 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 130 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 416 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 chunk 68 optimal weight: 0.0060 chunk 255 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 386 optimal weight: 50.0000 chunk 81 optimal weight: 7.9990 chunk 379 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 345 optimal weight: 9.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 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** D 7 ASN D 106 ASN H 37 GLN I 53 ASN ** I 59 HIS ** 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** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 223 ASN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN ** M 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 223 ASN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 296 ASN ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.093808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.079085 restraints weight = 162233.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.081346 restraints weight = 98620.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.082913 restraints weight = 67704.328| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4000 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= 0.166 Angle : 0.661 11.293 47821 Z= 0.334 Chirality : 0.045 0.200 5505 Planarity : 0.004 0.052 5856 Dihedral : 13.375 179.125 5545 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.90 % Favored : 90.88 % Rotamer: Outliers : 2.62 % Allowed : 18.31 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.13), residues: 4144 helix: -0.74 (0.15), residues: 1292 sheet: -0.60 (0.22), residues: 572 loop : -2.39 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 105 HIS 0.012 0.002 HIS C 165 PHE 0.026 0.002 PHE Q 82 TYR 0.031 0.002 TYR D 11 ARG 0.008 0.001 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 864) hydrogen bonds : angle 5.01835 ( 2380) SS BOND : bond 0.00310 ( 6) SS BOND : angle 0.57253 ( 12) covalent geometry : bond 0.00365 (35025) covalent geometry : angle 0.66127 (47809) *********************** 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 561 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 471 time to evaluate : 3.933 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 58 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8530 (mm) REVERT: C 60 ASP cc_start: 0.8936 (m-30) cc_final: 0.8645 (m-30) REVERT: C 131 MET cc_start: 0.8950 (tmm) cc_final: 0.8640 (tmm) REVERT: C 177 ASP cc_start: 0.8954 (p0) cc_final: 0.8044 (t70) REVERT: C 185 GLN cc_start: 0.7846 (pm20) cc_final: 0.7314 (pp30) REVERT: C 205 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5586 (mtt) REVERT: C 308 MET cc_start: 0.7686 (mpp) cc_final: 0.6891 (mpp) REVERT: C 312 LEU cc_start: 0.9167 (tp) cc_final: 0.8938 (tp) REVERT: D 48 LEU cc_start: 0.8769 (tp) cc_final: 0.8493 (tp) REVERT: D 89 ASP cc_start: 0.7580 (t0) cc_final: 0.7222 (p0) REVERT: E 46 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9016 (mmmm) REVERT: E 53 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6657 (mmmm) REVERT: E 86 ASN cc_start: 0.8059 (p0) cc_final: 0.7772 (t0) REVERT: F 46 LYS cc_start: 0.9269 (mttt) cc_final: 0.9024 (tptt) REVERT: G 29 ASP cc_start: 0.7997 (m-30) cc_final: 0.7519 (m-30) REVERT: G 42 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8838 (tm-30) REVERT: G 72 GLU cc_start: 0.8081 (pm20) cc_final: 0.7833 (pm20) REVERT: G 86 ASN cc_start: 0.9061 (p0) cc_final: 0.8846 (p0) REVERT: H 41 LEU cc_start: 0.6071 (mt) cc_final: 0.5461 (pp) REVERT: I 1 MET cc_start: 0.7396 (mmm) cc_final: 0.6481 (tpp) REVERT: I 306 VAL cc_start: 0.9204 (t) cc_final: 0.8864 (p) REVERT: J 119 ASP cc_start: 0.7567 (t0) cc_final: 0.7036 (t0) REVERT: J 135 LEU cc_start: 0.8652 (mm) cc_final: 0.8333 (mm) REVERT: J 183 MET cc_start: 0.4921 (ppp) cc_final: 0.4407 (ppp) REVERT: J 213 VAL cc_start: 0.8034 (m) cc_final: 0.7813 (m) REVERT: J 232 LYS cc_start: 0.8505 (tttt) cc_final: 0.7946 (tptt) REVERT: J 285 ASP cc_start: 0.7490 (p0) cc_final: 0.7204 (p0) REVERT: K 54 MET cc_start: 0.9010 (tpt) cc_final: 0.8737 (tpp) REVERT: K 111 ILE cc_start: 0.8621 (mt) cc_final: 0.8347 (mt) REVERT: K 218 ASN cc_start: 0.8267 (m-40) cc_final: 0.7933 (m-40) REVERT: L 63 PHE cc_start: 0.7597 (t80) cc_final: 0.7246 (t80) REVERT: L 166 ASP cc_start: 0.6125 (t0) cc_final: 0.5542 (p0) REVERT: L 207 ILE cc_start: 0.8127 (mm) cc_final: 0.7845 (mm) REVERT: M 1 MET cc_start: 0.7591 (mmm) cc_final: 0.6515 (mtt) REVERT: M 318 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7764 (tm-30) REVERT: N 2 TYR cc_start: 0.7557 (m-80) cc_final: 0.7328 (m-80) REVERT: N 54 MET cc_start: 0.6459 (mmt) cc_final: 0.6208 (mmt) REVERT: N 59 HIS cc_start: 0.9433 (t-90) cc_final: 0.9066 (t-90) REVERT: N 334 LYS cc_start: 0.8267 (pttt) cc_final: 0.7653 (mmtt) REVERT: O 31 LYS cc_start: 0.7797 (mppt) cc_final: 0.7567 (mmtm) REVERT: P 10 PHE cc_start: 0.8252 (p90) cc_final: 0.7999 (p90) REVERT: P 85 ILE cc_start: 0.8928 (tt) cc_final: 0.8674 (tp) REVERT: P 89 PHE cc_start: 0.8304 (m-10) cc_final: 0.8100 (m-10) REVERT: P 172 PHE cc_start: 0.8270 (m-80) cc_final: 0.7570 (m-80) REVERT: A 56 PHE cc_start: 0.7591 (m-10) cc_final: 0.7184 (t80) REVERT: A 107 LEU cc_start: 0.9347 (tp) cc_final: 0.9109 (pp) REVERT: A 118 LEU cc_start: 0.8456 (tp) cc_final: 0.8125 (tp) REVERT: A 140 LEU cc_start: 0.8549 (pp) cc_final: 0.8109 (mm) REVERT: A 143 HIS cc_start: 0.5833 (OUTLIER) cc_final: 0.5591 (m90) REVERT: A 177 MET cc_start: 0.6438 (mmt) cc_final: 0.5914 (mmt) REVERT: A 236 LEU cc_start: 0.6268 (mm) cc_final: 0.6033 (tp) REVERT: A 246 ASN cc_start: 0.8784 (m110) cc_final: 0.8373 (p0) REVERT: Q 27 ASN cc_start: 0.8749 (t0) cc_final: 0.8423 (t0) REVERT: Q 50 ASP cc_start: 0.8292 (m-30) cc_final: 0.8060 (m-30) REVERT: Q 115 MET cc_start: 0.8783 (mmp) cc_final: 0.8512 (mmm) REVERT: Q 149 MET cc_start: 0.4826 (pmm) cc_final: 0.4427 (pmm) REVERT: Q 161 LYS cc_start: 0.8497 (mmtm) cc_final: 0.7973 (tmmt) outliers start: 90 outliers final: 51 residues processed: 529 average time/residue: 0.4469 time to fit residues: 392.0714 Evaluate side-chains 475 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 420 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 ASN 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 29 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 5 ILE 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 J residue 311 VAL Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 3 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 204 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 322 VAL 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 133 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 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 243 ASP Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 289 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 379 optimal weight: 8.9990 chunk 387 optimal weight: 40.0000 chunk 314 optimal weight: 6.9990 chunk 404 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 403 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 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** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** 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** M 223 ASN ** 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 ** O 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.089143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.074320 restraints weight = 163032.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.076524 restraints weight = 97792.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.078038 restraints weight = 66887.889| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35031 Z= 0.207 Angle : 0.696 9.579 47821 Z= 0.355 Chirality : 0.046 0.239 5505 Planarity : 0.004 0.047 5856 Dihedral : 13.465 179.671 5545 Min Nonbonded Distance : 1.044 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.19 % Favored : 90.61 % Rotamer: Outliers : 3.15 % Allowed : 19.50 % Favored : 77.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.13), residues: 4144 helix: -0.72 (0.14), residues: 1312 sheet: -0.69 (0.22), residues: 579 loop : -2.31 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 58 HIS 0.014 0.002 HIS J 14 PHE 0.032 0.002 PHE C 282 TYR 0.027 0.002 TYR D 11 ARG 0.013 0.001 ARG D 6 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 864) hydrogen bonds : angle 5.08251 ( 2380) SS BOND : bond 0.01108 ( 6) SS BOND : angle 0.64339 ( 12) covalent geometry : bond 0.00449 (35025) covalent geometry : angle 0.69607 (47809) *********************** 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 565 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 457 time to evaluate : 3.773 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 52 GLU cc_start: 0.8469 (tp30) cc_final: 0.8175 (tp30) REVERT: C 131 MET cc_start: 0.9011 (tmm) cc_final: 0.8698 (tmm) REVERT: C 177 ASP cc_start: 0.9003 (p0) cc_final: 0.8063 (t70) REVERT: C 205 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.5724 (mtt) REVERT: C 308 MET cc_start: 0.7869 (mpp) cc_final: 0.7025 (mpp) REVERT: C 312 LEU cc_start: 0.9176 (tp) cc_final: 0.8941 (tp) REVERT: D 89 ASP cc_start: 0.7694 (t0) cc_final: 0.7382 (p0) REVERT: E 46 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9012 (mmmm) REVERT: E 53 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7002 (mttm) REVERT: E 88 LYS cc_start: 0.9025 (tptt) cc_final: 0.8752 (tppt) REVERT: F 46 LYS cc_start: 0.9313 (mttt) cc_final: 0.8986 (tptt) REVERT: G 21 GLU cc_start: 0.6928 (mp0) cc_final: 0.6516 (mp0) REVERT: G 29 ASP cc_start: 0.8042 (m-30) cc_final: 0.7558 (m-30) REVERT: G 42 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8737 (tm-30) REVERT: H 29 ASP cc_start: 0.8403 (t70) cc_final: 0.8196 (t0) REVERT: H 41 LEU cc_start: 0.5864 (mt) cc_final: 0.5260 (pp) REVERT: H 49 ARG cc_start: 0.8764 (ptm160) cc_final: 0.8416 (ptp90) REVERT: I 1 MET cc_start: 0.7607 (mmm) cc_final: 0.7210 (tpp) REVERT: I 54 MET cc_start: 0.8817 (mmp) cc_final: 0.8404 (mmm) REVERT: I 246 LEU cc_start: 0.8965 (mm) cc_final: 0.8683 (mp) REVERT: I 315 GLU cc_start: 0.8226 (pt0) cc_final: 0.7970 (pm20) REVERT: J 119 ASP cc_start: 0.7477 (t0) cc_final: 0.6939 (t0) REVERT: J 183 MET cc_start: 0.5263 (ppp) cc_final: 0.4742 (ppp) REVERT: J 213 VAL cc_start: 0.8264 (m) cc_final: 0.7760 (m) REVERT: J 285 ASP cc_start: 0.7455 (p0) cc_final: 0.7175 (p0) REVERT: K 54 MET cc_start: 0.9105 (tpt) cc_final: 0.8766 (tpp) REVERT: K 104 GLN cc_start: 0.8136 (mm110) cc_final: 0.7857 (mm110) REVERT: K 218 ASN cc_start: 0.8164 (m-40) cc_final: 0.7807 (m-40) REVERT: L 54 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8083 (mmp) REVERT: L 63 PHE cc_start: 0.8070 (t80) cc_final: 0.7693 (t80) REVERT: L 166 ASP cc_start: 0.6197 (t0) cc_final: 0.5543 (p0) REVERT: L 260 VAL cc_start: 0.8789 (t) cc_final: 0.8565 (t) REVERT: M 196 PHE cc_start: 0.7668 (p90) cc_final: 0.7285 (p90) REVERT: M 217 GLU cc_start: 0.7687 (mp0) cc_final: 0.7001 (pp20) REVERT: M 269 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.7876 (tp) REVERT: M 318 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7720 (tm-30) REVERT: N 1 MET cc_start: 0.7439 (pmm) cc_final: 0.7226 (pmm) REVERT: N 2 TYR cc_start: 0.7825 (m-80) cc_final: 0.7462 (m-80) REVERT: N 54 MET cc_start: 0.6674 (mmt) cc_final: 0.6435 (mmt) REVERT: N 104 GLN cc_start: 0.8345 (pp30) cc_final: 0.8118 (pp30) REVERT: N 334 LYS cc_start: 0.8382 (pttt) cc_final: 0.8124 (pttm) REVERT: O 2 TYR cc_start: 0.7961 (m-80) cc_final: 0.7605 (m-80) REVERT: P 10 PHE cc_start: 0.8464 (p90) cc_final: 0.8086 (p90) REVERT: P 12 PHE cc_start: 0.8634 (m-80) cc_final: 0.8229 (m-80) REVERT: P 85 ILE cc_start: 0.9066 (tt) cc_final: 0.8842 (tp) REVERT: P 89 PHE cc_start: 0.8228 (m-10) cc_final: 0.7963 (m-10) REVERT: P 172 PHE cc_start: 0.8622 (m-80) cc_final: 0.7481 (m-80) REVERT: A 56 PHE cc_start: 0.7660 (m-10) cc_final: 0.7242 (t80) REVERT: A 107 LEU cc_start: 0.9351 (tp) cc_final: 0.9113 (pp) REVERT: A 118 LEU cc_start: 0.8394 (tp) cc_final: 0.8114 (tp) REVERT: A 140 LEU cc_start: 0.8640 (pp) cc_final: 0.8200 (mm) REVERT: A 177 MET cc_start: 0.6507 (mmt) cc_final: 0.5892 (mmt) REVERT: A 236 LEU cc_start: 0.6863 (mm) cc_final: 0.6496 (tp) REVERT: Q 2 SER cc_start: 0.4930 (m) cc_final: 0.4639 (p) REVERT: Q 27 ASN cc_start: 0.8938 (t0) cc_final: 0.8626 (t0) REVERT: Q 115 MET cc_start: 0.8753 (mmp) cc_final: 0.8462 (mmt) REVERT: Q 149 MET cc_start: 0.5060 (pmm) cc_final: 0.4708 (pmm) REVERT: Q 161 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8127 (tmmt) REVERT: Q 169 LYS cc_start: 0.0836 (OUTLIER) cc_final: -0.1337 (ptmm) outliers start: 108 outliers final: 66 residues processed: 526 average time/residue: 0.4517 time to fit residues: 395.5804 Evaluate side-chains 473 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 402 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 MET Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 12 LEU 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 29 ASP Chi-restraints excluded: chain F residue 44 VAL 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 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 3 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain L residue 9 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 266 LEU Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 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 146 ASP Chi-restraints excluded: chain N residue 242 LEU 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 133 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 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 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 228 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain Q residue 169 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 267 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 334 optimal weight: 10.0000 chunk 416 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 234 optimal weight: 0.9980 chunk 395 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.090843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.076057 restraints weight = 161482.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.078313 restraints weight = 96530.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.079859 restraints weight = 65829.461| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35031 Z= 0.134 Angle : 0.672 10.982 47821 Z= 0.332 Chirality : 0.045 0.304 5505 Planarity : 0.004 0.060 5856 Dihedral : 13.451 179.779 5545 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.37 % Favored : 91.43 % Rotamer: Outliers : 3.00 % Allowed : 20.64 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.13), residues: 4144 helix: -0.63 (0.15), residues: 1298 sheet: -0.73 (0.22), residues: 579 loop : -2.27 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP Q 22 HIS 0.009 0.002 HIS C 165 PHE 0.025 0.002 PHE N 60 TYR 0.025 0.002 TYR A 484 ARG 0.009 0.000 ARG Q 180 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 864) hydrogen bonds : angle 4.97672 ( 2380) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.47989 ( 12) covalent geometry : bond 0.00302 (35025) covalent geometry : angle 0.67194 (47809) *********************** 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 555 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 452 time to evaluate : 3.585 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: 0.8450 (tp30) cc_final: 0.8148 (tp30) REVERT: C 58 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8600 (mm) REVERT: C 131 MET cc_start: 0.9023 (tmm) cc_final: 0.8639 (tmm) REVERT: C 177 ASP cc_start: 0.9007 (p0) cc_final: 0.8054 (t70) REVERT: C 205 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5257 (mtt) REVERT: C 308 MET cc_start: 0.7870 (mpp) cc_final: 0.7114 (mpp) REVERT: C 312 LEU cc_start: 0.9159 (tp) cc_final: 0.8910 (tp) REVERT: D 12 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8771 (mm) REVERT: D 89 ASP cc_start: 0.7734 (t0) cc_final: 0.7426 (p0) REVERT: E 46 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9107 (mmmm) REVERT: E 53 LYS cc_start: 0.7310 (ptmm) cc_final: 0.6789 (mttm) REVERT: E 88 LYS cc_start: 0.9021 (tptt) cc_final: 0.8665 (tppt) REVERT: F 46 LYS cc_start: 0.9341 (mttt) cc_final: 0.8993 (tptt) REVERT: G 21 GLU cc_start: 0.6659 (mp0) cc_final: 0.6375 (mp0) REVERT: G 29 ASP cc_start: 0.8018 (m-30) cc_final: 0.7453 (m-30) REVERT: G 42 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8736 (tm-30) REVERT: G 56 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7436 (pptt) REVERT: G 57 LYS cc_start: 0.7600 (mtmm) cc_final: 0.6977 (mmmt) REVERT: H 41 LEU cc_start: 0.5735 (mt) cc_final: 0.5178 (pp) REVERT: H 49 ARG cc_start: 0.8784 (ptm160) cc_final: 0.8484 (ptp90) REVERT: I 1 MET cc_start: 0.7711 (mmm) cc_final: 0.7307 (tpp) REVERT: I 54 MET cc_start: 0.8588 (mmp) cc_final: 0.8211 (mmm) REVERT: I 145 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: I 315 GLU cc_start: 0.8194 (pt0) cc_final: 0.7948 (pm20) REVERT: J 119 ASP cc_start: 0.7698 (t0) cc_final: 0.7141 (t0) REVERT: J 135 LEU cc_start: 0.8820 (mm) cc_final: 0.8416 (mm) REVERT: J 213 VAL cc_start: 0.8218 (m) cc_final: 0.7999 (m) REVERT: J 285 ASP cc_start: 0.7555 (p0) cc_final: 0.7269 (p0) REVERT: J 334 LYS cc_start: 0.8604 (pptt) cc_final: 0.8062 (pttm) REVERT: K 54 MET cc_start: 0.8968 (tpt) cc_final: 0.8619 (tpp) REVERT: K 218 ASN cc_start: 0.8335 (m-40) cc_final: 0.8015 (m-40) REVERT: L 54 MET cc_start: 0.7982 (mmp) cc_final: 0.7586 (mmp) REVERT: L 63 PHE cc_start: 0.8075 (t80) cc_final: 0.7689 (t80) REVERT: L 166 ASP cc_start: 0.5963 (t0) cc_final: 0.5283 (p0) REVERT: L 260 VAL cc_start: 0.8693 (t) cc_final: 0.8470 (t) REVERT: M 1 MET cc_start: 0.8028 (mmm) cc_final: 0.7368 (mtt) REVERT: M 19 GLN cc_start: 0.7934 (mp10) cc_final: 0.7311 (mp10) REVERT: M 196 PHE cc_start: 0.7565 (p90) cc_final: 0.7319 (p90) REVERT: M 217 GLU cc_start: 0.7643 (mp0) cc_final: 0.6978 (pp20) REVERT: M 318 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7473 (tm-30) REVERT: N 2 TYR cc_start: 0.7943 (m-80) cc_final: 0.7544 (m-80) REVERT: N 54 MET cc_start: 0.6651 (mmt) cc_final: 0.6400 (mmt) REVERT: N 104 GLN cc_start: 0.8301 (pp30) cc_final: 0.8082 (pp30) REVERT: N 334 LYS cc_start: 0.8362 (pttt) cc_final: 0.8095 (pttm) REVERT: P 10 PHE cc_start: 0.8286 (p90) cc_final: 0.7981 (p90) REVERT: P 137 LEU cc_start: 0.8490 (mt) cc_final: 0.8185 (pp) REVERT: P 141 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7295 (mpp) REVERT: P 172 PHE cc_start: 0.8676 (m-80) cc_final: 0.7791 (m-80) REVERT: A 31 MET cc_start: 0.8053 (ptm) cc_final: 0.7774 (ptm) REVERT: A 56 PHE cc_start: 0.7614 (m-10) cc_final: 0.7246 (t80) REVERT: A 107 LEU cc_start: 0.9349 (tp) cc_final: 0.9096 (pp) REVERT: A 118 LEU cc_start: 0.8408 (tp) cc_final: 0.8100 (tp) REVERT: A 140 LEU cc_start: 0.8637 (pp) cc_final: 0.8318 (mm) REVERT: A 143 HIS cc_start: 0.5922 (OUTLIER) cc_final: 0.5700 (m90) REVERT: A 177 MET cc_start: 0.6448 (mmt) cc_final: 0.6013 (mmm) REVERT: A 236 LEU cc_start: 0.6918 (mm) cc_final: 0.6522 (tp) REVERT: A 343 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8027 (tp) REVERT: Q 2 SER cc_start: 0.4901 (m) cc_final: 0.4667 (p) REVERT: Q 27 ASN cc_start: 0.8959 (t0) cc_final: 0.8634 (t0) REVERT: Q 149 MET cc_start: 0.4829 (pmm) cc_final: 0.4542 (pmm) REVERT: Q 161 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8022 (tmmt) outliers start: 103 outliers final: 66 residues processed: 516 average time/residue: 0.4689 time to fit residues: 400.1544 Evaluate side-chains 480 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 406 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 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 205 MET Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 4 TRP 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 56 LYS 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 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 55 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 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 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 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 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 141 MET 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 136 PHE 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 442 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 220 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 232 optimal weight: 0.0970 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 8 optimal weight: 0.0000 chunk 325 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 HIS ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.091667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.076877 restraints weight = 161632.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.079154 restraints weight = 96558.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.080704 restraints weight = 65811.203| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35031 Z= 0.125 Angle : 0.669 13.752 47821 Z= 0.327 Chirality : 0.045 0.254 5505 Planarity : 0.004 0.063 5856 Dihedral : 13.439 179.542 5545 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.71 % Favored : 91.10 % Rotamer: Outliers : 2.59 % Allowed : 21.46 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.13), residues: 4144 helix: -0.54 (0.15), residues: 1294 sheet: -0.66 (0.23), residues: 550 loop : -2.26 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 100 HIS 0.008 0.001 HIS C 228 PHE 0.027 0.002 PHE N 60 TYR 0.023 0.001 TYR C 20 ARG 0.006 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 864) hydrogen bonds : angle 4.92005 ( 2380) SS BOND : bond 0.00136 ( 6) SS BOND : angle 0.43622 ( 12) covalent geometry : bond 0.00282 (35025) covalent geometry : angle 0.66864 (47809) *********************** 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 538 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 449 time to evaluate : 3.776 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 52 GLU cc_start: 0.8562 (tp30) cc_final: 0.8277 (tp30) REVERT: C 58 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8612 (mm) REVERT: C 131 MET cc_start: 0.9032 (tmm) cc_final: 0.8652 (tmm) REVERT: C 205 MET cc_start: 0.5784 (OUTLIER) cc_final: 0.4925 (mtt) REVERT: C 308 MET cc_start: 0.7882 (mpp) cc_final: 0.7159 (mpp) REVERT: C 312 LEU cc_start: 0.9131 (tp) cc_final: 0.8883 (tp) REVERT: D 12 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8692 (mm) REVERT: D 89 ASP cc_start: 0.7725 (t0) cc_final: 0.7376 (p0) REVERT: E 46 LYS cc_start: 0.9428 (mmmm) cc_final: 0.9040 (mmmm) REVERT: E 53 LYS cc_start: 0.7477 (ptmm) cc_final: 0.7012 (mttm) REVERT: E 88 LYS cc_start: 0.8917 (tptt) cc_final: 0.8598 (tppt) REVERT: F 46 LYS cc_start: 0.9336 (mttt) cc_final: 0.8849 (tptt) REVERT: G 29 ASP cc_start: 0.8094 (m-30) cc_final: 0.7699 (m-30) REVERT: G 42 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8710 (tm-30) REVERT: G 54 LEU cc_start: 0.7230 (tp) cc_final: 0.6484 (tp) REVERT: G 57 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7065 (tptp) REVERT: H 41 LEU cc_start: 0.5858 (mt) cc_final: 0.5278 (pp) REVERT: H 49 ARG cc_start: 0.8770 (ptm160) cc_final: 0.8437 (ptp90) REVERT: I 1 MET cc_start: 0.7722 (mmm) cc_final: 0.7269 (tpp) REVERT: I 54 MET cc_start: 0.8630 (mmp) cc_final: 0.8259 (mmm) REVERT: I 145 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: I 315 GLU cc_start: 0.8177 (pt0) cc_final: 0.7942 (pm20) REVERT: J 88 PHE cc_start: 0.8360 (m-80) cc_final: 0.6834 (m-80) REVERT: J 119 ASP cc_start: 0.7648 (t0) cc_final: 0.7094 (t0) REVERT: J 135 LEU cc_start: 0.8765 (mm) cc_final: 0.8386 (mm) REVERT: J 213 VAL cc_start: 0.7946 (m) cc_final: 0.7653 (m) REVERT: J 250 ILE cc_start: 0.9223 (mm) cc_final: 0.8752 (mp) REVERT: J 285 ASP cc_start: 0.7568 (p0) cc_final: 0.7332 (p0) REVERT: J 334 LYS cc_start: 0.8653 (pptt) cc_final: 0.8120 (ptpp) REVERT: K 54 MET cc_start: 0.8854 (tpt) cc_final: 0.8583 (tpp) REVERT: K 196 PHE cc_start: 0.7622 (p90) cc_final: 0.7187 (p90) REVERT: K 218 ASN cc_start: 0.8341 (m-40) cc_final: 0.8020 (m-40) REVERT: L 54 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7564 (mmp) REVERT: L 63 PHE cc_start: 0.7990 (t80) cc_final: 0.7579 (t80) REVERT: L 166 ASP cc_start: 0.6044 (t0) cc_final: 0.5405 (p0) REVERT: L 260 VAL cc_start: 0.8585 (t) cc_final: 0.8371 (t) REVERT: M 1 MET cc_start: 0.7990 (mmm) cc_final: 0.7346 (mtt) REVERT: M 19 GLN cc_start: 0.7986 (mp10) cc_final: 0.7322 (mp10) REVERT: M 196 PHE cc_start: 0.7561 (p90) cc_final: 0.7242 (p90) REVERT: M 217 GLU cc_start: 0.7669 (mp0) cc_final: 0.7045 (pp20) REVERT: M 318 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7507 (tm-30) REVERT: N 2 TYR cc_start: 0.7951 (m-80) cc_final: 0.7458 (m-80) REVERT: N 104 GLN cc_start: 0.8274 (pp30) cc_final: 0.8068 (pp30) REVERT: N 334 LYS cc_start: 0.8299 (pttt) cc_final: 0.8020 (pttm) REVERT: P 10 PHE cc_start: 0.8177 (p90) cc_final: 0.7926 (p90) REVERT: P 12 PHE cc_start: 0.8408 (m-80) cc_final: 0.8061 (m-80) REVERT: P 28 LEU cc_start: 0.9127 (mp) cc_final: 0.8919 (mt) REVERT: P 42 LEU cc_start: 0.8806 (mm) cc_final: 0.8593 (mp) REVERT: P 137 LEU cc_start: 0.8503 (mt) cc_final: 0.8158 (pp) REVERT: P 141 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7367 (mpp) REVERT: P 172 PHE cc_start: 0.8665 (m-80) cc_final: 0.7813 (m-80) REVERT: A 56 PHE cc_start: 0.7605 (m-10) cc_final: 0.7270 (t80) REVERT: A 107 LEU cc_start: 0.9343 (tp) cc_final: 0.9087 (pp) REVERT: A 118 LEU cc_start: 0.8473 (tp) cc_final: 0.8116 (tp) REVERT: A 136 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: A 138 TYR cc_start: 0.8560 (t80) cc_final: 0.8302 (t80) REVERT: A 140 LEU cc_start: 0.8604 (pp) cc_final: 0.7994 (mm) REVERT: A 143 HIS cc_start: 0.5950 (OUTLIER) cc_final: 0.5679 (m90) REVERT: A 177 MET cc_start: 0.6383 (mmt) cc_final: 0.5925 (mmm) REVERT: A 236 LEU cc_start: 0.6785 (mm) cc_final: 0.6467 (tp) REVERT: A 246 ASN cc_start: 0.8762 (m110) cc_final: 0.8469 (p0) REVERT: A 343 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7994 (tp) REVERT: Q 2 SER cc_start: 0.4895 (m) cc_final: 0.4673 (p) REVERT: Q 27 ASN cc_start: 0.8994 (t0) cc_final: 0.8669 (t0) REVERT: Q 82 PHE cc_start: 0.6586 (t80) cc_final: 0.6308 (t80) REVERT: Q 115 MET cc_start: 0.8751 (mmp) cc_final: 0.8478 (mmt) REVERT: Q 149 MET cc_start: 0.4863 (pmm) cc_final: 0.4562 (pmm) REVERT: Q 161 LYS cc_start: 0.8555 (mmtm) cc_final: 0.8040 (tmmt) outliers start: 89 outliers final: 57 residues processed: 499 average time/residue: 0.4861 time to fit residues: 403.1512 Evaluate side-chains 481 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 415 time to evaluate : 3.800 ------------------------------------------------------------------------------- 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 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 12 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 16 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 5 ILE Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 242 LEU 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 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 136 VAL 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 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 116 THR Chi-restraints excluded: chain P residue 141 MET 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 136 PHE 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 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 442 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 87 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 370 optimal weight: 0.0000 chunk 314 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 318 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** 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 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 290 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 = 0.3978 r_free = 0.3978 target = 0.089557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.074779 restraints weight = 160957.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.076991 restraints weight = 95421.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.078520 restraints weight = 65066.196| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5390 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= 0.146 Angle : 0.672 14.636 47821 Z= 0.332 Chirality : 0.045 0.277 5505 Planarity : 0.004 0.060 5856 Dihedral : 13.454 178.965 5545 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.86 % Favored : 90.88 % Rotamer: Outliers : 2.86 % Allowed : 21.60 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.13), residues: 4144 helix: -0.52 (0.15), residues: 1311 sheet: -0.88 (0.22), residues: 569 loop : -2.22 (0.12), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 58 HIS 0.008 0.001 HIS C 165 PHE 0.028 0.002 PHE N 60 TYR 0.022 0.001 TYR C 20 ARG 0.007 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 864) hydrogen bonds : angle 4.95074 ( 2380) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.51067 ( 12) covalent geometry : bond 0.00328 (35025) covalent geometry : angle 0.67184 (47809) *********************** 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 522 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 424 time to evaluate : 3.969 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: 0.8915 (OUTLIER) cc_final: 0.8551 (mm) REVERT: C 131 MET cc_start: 0.9029 (tmm) cc_final: 0.8617 (tmm) REVERT: C 205 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5093 (mtt) REVERT: C 308 MET cc_start: 0.7943 (mpp) cc_final: 0.7159 (mpp) REVERT: C 312 LEU cc_start: 0.9161 (tp) cc_final: 0.8919 (tp) REVERT: D 12 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8726 (mm) REVERT: D 89 ASP cc_start: 0.7735 (t0) cc_final: 0.7444 (p0) REVERT: E 53 LYS cc_start: 0.7361 (ptmm) cc_final: 0.6946 (mttm) REVERT: E 88 LYS cc_start: 0.8991 (tptt) cc_final: 0.8666 (tppt) REVERT: F 46 LYS cc_start: 0.9297 (mttt) cc_final: 0.8988 (tptt) REVERT: G 29 ASP cc_start: 0.8048 (m-30) cc_final: 0.7568 (m-30) REVERT: G 42 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8712 (tm-30) REVERT: H 41 LEU cc_start: 0.5984 (mt) cc_final: 0.5342 (pp) REVERT: H 49 ARG cc_start: 0.8803 (ptm160) cc_final: 0.8492 (ptp90) REVERT: I 1 MET cc_start: 0.7819 (mmm) cc_final: 0.7561 (tpp) REVERT: I 54 MET cc_start: 0.8758 (mmp) cc_final: 0.8391 (mmm) REVERT: I 145 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: I 315 GLU cc_start: 0.8259 (pt0) cc_final: 0.8035 (pm20) REVERT: J 107 ASP cc_start: 0.7670 (t0) cc_final: 0.7365 (t70) REVERT: J 119 ASP cc_start: 0.7685 (t0) cc_final: 0.7060 (t0) REVERT: J 213 VAL cc_start: 0.8109 (m) cc_final: 0.7839 (m) REVERT: J 232 LYS cc_start: 0.8600 (tttt) cc_final: 0.8121 (tptt) REVERT: J 250 ILE cc_start: 0.9270 (mm) cc_final: 0.8840 (mp) REVERT: J 285 ASP cc_start: 0.7581 (p0) cc_final: 0.7328 (p0) REVERT: J 334 LYS cc_start: 0.8715 (pptt) cc_final: 0.8304 (ptpt) REVERT: K 54 MET cc_start: 0.8917 (tpt) cc_final: 0.8684 (tpp) REVERT: K 218 ASN cc_start: 0.8412 (m-40) cc_final: 0.8085 (m-40) REVERT: L 54 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7937 (mmp) REVERT: L 63 PHE cc_start: 0.8150 (t80) cc_final: 0.7762 (t80) REVERT: L 166 ASP cc_start: 0.5959 (t0) cc_final: 0.5240 (p0) REVERT: L 260 VAL cc_start: 0.8741 (t) cc_final: 0.8526 (t) REVERT: M 1 MET cc_start: 0.8075 (mmm) cc_final: 0.7486 (mtt) REVERT: M 19 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: M 28 GLU cc_start: 0.8385 (pp20) cc_final: 0.7752 (pp20) REVERT: M 196 PHE cc_start: 0.7545 (p90) cc_final: 0.7234 (p90) REVERT: M 217 GLU cc_start: 0.7693 (mp0) cc_final: 0.7179 (pp20) REVERT: M 275 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7723 (mm) REVERT: M 318 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7619 (tm-30) REVERT: N 2 TYR cc_start: 0.7898 (m-80) cc_final: 0.7603 (m-80) REVERT: N 104 GLN cc_start: 0.8324 (pp30) cc_final: 0.8004 (pp30) REVERT: N 160 ILE cc_start: 0.9005 (pt) cc_final: 0.8773 (mp) REVERT: O 198 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8397 (mm) REVERT: P 10 PHE cc_start: 0.8254 (p90) cc_final: 0.7951 (p90) REVERT: P 172 PHE cc_start: 0.8750 (m-80) cc_final: 0.7820 (m-80) REVERT: A 56 PHE cc_start: 0.7676 (m-10) cc_final: 0.7313 (t80) REVERT: A 107 LEU cc_start: 0.9353 (tp) cc_final: 0.9093 (pp) REVERT: A 118 LEU cc_start: 0.8474 (tp) cc_final: 0.8178 (tp) REVERT: A 138 TYR cc_start: 0.8506 (t80) cc_final: 0.8279 (t80) REVERT: A 140 LEU cc_start: 0.8637 (pp) cc_final: 0.8103 (mm) REVERT: A 143 HIS cc_start: 0.6032 (OUTLIER) cc_final: 0.5741 (m90) REVERT: A 177 MET cc_start: 0.6487 (mmt) cc_final: 0.5950 (mmp) REVERT: A 236 LEU cc_start: 0.7274 (mm) cc_final: 0.6953 (tp) REVERT: A 343 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8016 (tp) REVERT: Q 2 SER cc_start: 0.5072 (m) cc_final: 0.4814 (p) REVERT: Q 27 ASN cc_start: 0.9051 (t0) cc_final: 0.8721 (t0) REVERT: Q 82 PHE cc_start: 0.6744 (t80) cc_final: 0.6522 (t80) REVERT: Q 115 MET cc_start: 0.8709 (mmp) cc_final: 0.8413 (mmt) REVERT: Q 149 MET cc_start: 0.4921 (pmm) cc_final: 0.4606 (pmm) REVERT: Q 161 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8139 (tmmt) outliers start: 98 outliers final: 73 residues processed: 490 average time/residue: 0.5101 time to fit residues: 418.8272 Evaluate side-chains 485 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 402 time to evaluate : 3.557 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 63 CYS 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 5 ILE 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 19 GLN Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 242 LEU 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 193 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 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 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 325 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 497 PHE 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 105 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 318 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 376 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN K 162 HIS ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 GLN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 223 ASN ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 310 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.081173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.066501 restraints weight = 164925.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.068521 restraints weight = 96528.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.069878 restraints weight = 65586.390| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 35031 Z= 0.281 Angle : 0.833 19.887 47821 Z= 0.427 Chirality : 0.050 0.366 5505 Planarity : 0.006 0.068 5856 Dihedral : 13.790 177.955 5545 Min Nonbonded Distance : 0.961 Molprobity Statistics. All-atom Clashscore : 29.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.83 % Favored : 88.92 % Rotamer: Outliers : 3.15 % Allowed : 21.60 % Favored : 75.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.13), residues: 4144 helix: -0.82 (0.14), residues: 1324 sheet: -1.06 (0.22), residues: 602 loop : -2.30 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP J 58 HIS 0.012 0.003 HIS L 57 PHE 0.034 0.003 PHE N 60 TYR 0.051 0.003 TYR I 72 ARG 0.013 0.001 ARG K 291 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 864) hydrogen bonds : angle 5.34707 ( 2380) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.88000 ( 12) covalent geometry : bond 0.00611 (35025) covalent geometry : angle 0.83331 (47809) *********************** 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 532 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 424 time to evaluate : 3.850 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 60 ASP cc_start: 0.9119 (m-30) cc_final: 0.8852 (m-30) REVERT: C 131 MET cc_start: 0.9011 (tmm) cc_final: 0.8536 (tmm) REVERT: C 138 MET cc_start: 0.6870 (mmp) cc_final: 0.6529 (mmp) REVERT: C 205 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.5914 (mtt) REVERT: C 312 LEU cc_start: 0.9293 (tp) cc_final: 0.9001 (tp) REVERT: D 89 ASP cc_start: 0.8066 (t0) cc_final: 0.7587 (p0) REVERT: D 95 VAL cc_start: 0.9534 (t) cc_final: 0.9307 (t) REVERT: E 53 LYS cc_start: 0.8219 (ptmm) cc_final: 0.7875 (mttm) REVERT: F 72 GLU cc_start: 0.8613 (tp30) cc_final: 0.8322 (tp30) REVERT: G 29 ASP cc_start: 0.8335 (m-30) cc_final: 0.7771 (m-30) REVERT: H 16 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7416 (m) REVERT: H 29 ASP cc_start: 0.8582 (t70) cc_final: 0.8355 (t70) REVERT: H 49 ARG cc_start: 0.8845 (ptm160) cc_final: 0.8515 (ptp90) REVERT: I 1 MET cc_start: 0.7943 (mmm) cc_final: 0.7596 (tpp) REVERT: I 31 LYS cc_start: 0.8209 (mmtp) cc_final: 0.7898 (mmtp) REVERT: I 54 MET cc_start: 0.8908 (mmp) cc_final: 0.8706 (mmm) REVERT: I 55 LEU cc_start: 0.9533 (mm) cc_final: 0.9263 (mt) REVERT: I 104 GLN cc_start: 0.8019 (tp40) cc_final: 0.6803 (tm-30) REVERT: I 246 LEU cc_start: 0.8969 (mm) cc_final: 0.8551 (mp) REVERT: I 315 GLU cc_start: 0.8621 (pt0) cc_final: 0.8208 (pm20) REVERT: J 107 ASP cc_start: 0.7827 (t0) cc_final: 0.7508 (t70) REVERT: J 119 ASP cc_start: 0.7885 (t0) cc_final: 0.7351 (t0) REVERT: J 183 MET cc_start: 0.5848 (ppp) cc_final: 0.5264 (ppp) REVERT: J 232 LYS cc_start: 0.8796 (tttt) cc_final: 0.8211 (tptt) REVERT: J 334 LYS cc_start: 0.9066 (pptt) cc_final: 0.8707 (ptpt) REVERT: K 196 PHE cc_start: 0.8161 (p90) cc_final: 0.7727 (p90) REVERT: K 218 ASN cc_start: 0.8607 (m-40) cc_final: 0.8334 (m-40) REVERT: L 63 PHE cc_start: 0.8792 (t80) cc_final: 0.8379 (t80) REVERT: L 166 ASP cc_start: 0.6343 (t0) cc_final: 0.5583 (p0) REVERT: L 335 MET cc_start: 0.8344 (ppp) cc_final: 0.7603 (ppp) REVERT: M 1 MET cc_start: 0.8287 (mmm) cc_final: 0.7823 (mtt) REVERT: M 19 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: M 39 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8107 (tm-30) REVERT: M 169 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6439 (pm20) REVERT: M 196 PHE cc_start: 0.8384 (p90) cc_final: 0.7983 (p90) REVERT: M 275 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8201 (mm) REVERT: M 318 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7765 (tm-30) REVERT: N 2 TYR cc_start: 0.8128 (m-80) cc_final: 0.7881 (m-80) REVERT: N 104 GLN cc_start: 0.8357 (pp30) cc_final: 0.8125 (pp30) REVERT: N 236 GLU cc_start: 0.8741 (pt0) cc_final: 0.8524 (pt0) REVERT: N 334 LYS cc_start: 0.8520 (pttt) cc_final: 0.8214 (pttm) REVERT: O 65 ASP cc_start: 0.8839 (m-30) cc_final: 0.8491 (p0) REVERT: P 10 PHE cc_start: 0.8647 (p90) cc_final: 0.8205 (p90) REVERT: P 12 PHE cc_start: 0.8683 (m-80) cc_final: 0.8235 (m-80) REVERT: P 172 PHE cc_start: 0.8966 (m-80) cc_final: 0.7798 (m-80) REVERT: P 251 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7473 (mt) REVERT: A 48 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7240 (m) REVERT: A 107 LEU cc_start: 0.9408 (tp) cc_final: 0.9144 (pp) REVERT: A 138 TYR cc_start: 0.8557 (t80) cc_final: 0.8311 (t80) REVERT: A 140 LEU cc_start: 0.8782 (pp) cc_final: 0.8295 (mm) REVERT: A 177 MET cc_start: 0.6743 (mmt) cc_final: 0.6128 (mmt) REVERT: Q 2 SER cc_start: 0.5928 (m) cc_final: 0.5688 (p) REVERT: Q 27 ASN cc_start: 0.8989 (t0) cc_final: 0.8703 (t0) REVERT: Q 50 ASP cc_start: 0.8360 (t0) cc_final: 0.7738 (m-30) REVERT: Q 84 HIS cc_start: 0.8363 (p90) cc_final: 0.8032 (p90) REVERT: Q 115 MET cc_start: 0.8720 (mmp) cc_final: 0.8263 (mmt) REVERT: Q 121 LEU cc_start: 0.8247 (tp) cc_final: 0.7932 (tp) REVERT: Q 149 MET cc_start: 0.4987 (pmm) cc_final: 0.4765 (pmm) REVERT: Q 154 SER cc_start: 0.8511 (t) cc_final: 0.8261 (m) REVERT: Q 161 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8322 (tmmt) REVERT: Q 213 TYR cc_start: 0.6884 (t80) cc_final: 0.6543 (t80) outliers start: 108 outliers final: 73 residues processed: 504 average time/residue: 0.4509 time to fit residues: 378.1230 Evaluate side-chains 450 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 370 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 99 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 9 ILE Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 242 LEU 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 193 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 275 ILE 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 51 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 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 325 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 136 TYR Chi-restraints excluded: chain P residue 251 LEU 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 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 363 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 442 ILE 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 337 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 398 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 GLN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 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** A 63 ASN ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.081804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.067860 restraints weight = 159304.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.069909 restraints weight = 91217.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.071291 restraints weight = 60848.292| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35031 Z= 0.212 Angle : 0.779 14.447 47821 Z= 0.389 Chirality : 0.049 0.304 5505 Planarity : 0.005 0.054 5856 Dihedral : 13.790 179.259 5545 Min Nonbonded Distance : 1.127 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.15 % Favored : 90.64 % Rotamer: Outliers : 2.48 % Allowed : 23.41 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.13), residues: 4144 helix: -0.83 (0.14), residues: 1329 sheet: -1.07 (0.22), residues: 601 loop : -2.32 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 100 HIS 0.012 0.002 HIS C 165 PHE 0.030 0.002 PHE N 60 TYR 0.034 0.002 TYR I 72 ARG 0.015 0.001 ARG J 221 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 864) hydrogen bonds : angle 5.28629 ( 2380) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.71189 ( 12) covalent geometry : bond 0.00473 (35025) covalent geometry : angle 0.77949 (47809) ********************** 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 502 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 417 time to evaluate : 5.656 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 131 MET cc_start: 0.9040 (tmm) cc_final: 0.8607 (tmm) REVERT: C 138 MET cc_start: 0.7000 (mmp) cc_final: 0.6690 (mmp) REVERT: C 205 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.5487 (mtt) REVERT: C 288 PHE cc_start: 0.8989 (t80) cc_final: 0.8624 (t80) REVERT: C 312 LEU cc_start: 0.9260 (tp) cc_final: 0.8957 (tp) REVERT: D 89 ASP cc_start: 0.7995 (t0) cc_final: 0.7504 (p0) REVERT: D 95 VAL cc_start: 0.9529 (t) cc_final: 0.9285 (t) REVERT: E 53 LYS cc_start: 0.8248 (ptmm) cc_final: 0.8026 (mttm) REVERT: F 72 GLU cc_start: 0.8596 (tp30) cc_final: 0.8287 (tp30) REVERT: G 21 GLU cc_start: 0.7090 (mp0) cc_final: 0.6103 (mp0) REVERT: G 29 ASP cc_start: 0.8244 (m-30) cc_final: 0.7709 (m-30) REVERT: G 42 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8707 (tm-30) REVERT: G 57 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7302 (mmmt) REVERT: G 84 LEU cc_start: 0.6778 (tt) cc_final: 0.6577 (tp) REVERT: H 12 LEU cc_start: 0.8689 (pp) cc_final: 0.8039 (tp) REVERT: H 49 ARG cc_start: 0.8868 (ptm160) cc_final: 0.8567 (ptp90) REVERT: I 1 MET cc_start: 0.7950 (mmm) cc_final: 0.7527 (tpp) REVERT: I 31 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7808 (mmtp) REVERT: I 54 MET cc_start: 0.8657 (mmp) cc_final: 0.8420 (mmp) REVERT: I 55 LEU cc_start: 0.9470 (mm) cc_final: 0.9181 (mt) REVERT: I 104 GLN cc_start: 0.8020 (tp40) cc_final: 0.6570 (tm-30) REVERT: I 246 LEU cc_start: 0.8953 (mm) cc_final: 0.8526 (mp) REVERT: J 54 MET cc_start: 0.8875 (tpp) cc_final: 0.8652 (tpp) REVERT: J 107 ASP cc_start: 0.7714 (t0) cc_final: 0.7393 (t70) REVERT: J 119 ASP cc_start: 0.7850 (t0) cc_final: 0.7321 (t0) REVERT: J 183 MET cc_start: 0.5483 (ppp) cc_final: 0.5071 (ppp) REVERT: J 334 LYS cc_start: 0.8997 (pptt) cc_final: 0.8681 (ptpt) REVERT: K 196 PHE cc_start: 0.8055 (p90) cc_final: 0.7647 (p90) REVERT: K 218 ASN cc_start: 0.8629 (m-40) cc_final: 0.8376 (m-40) REVERT: L 63 PHE cc_start: 0.8552 (t80) cc_final: 0.8079 (t80) REVERT: L 166 ASP cc_start: 0.6335 (t0) cc_final: 0.5624 (p0) REVERT: L 239 LEU cc_start: 0.8904 (mt) cc_final: 0.8582 (tp) REVERT: L 260 VAL cc_start: 0.9087 (t) cc_final: 0.8849 (t) REVERT: L 335 MET cc_start: 0.8412 (ppp) cc_final: 0.7763 (ppp) REVERT: M 1 MET cc_start: 0.8186 (mmm) cc_final: 0.7689 (mtt) REVERT: M 39 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8065 (tm-30) REVERT: M 169 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: M 196 PHE cc_start: 0.8441 (p90) cc_final: 0.7963 (p90) REVERT: M 275 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8147 (mm) REVERT: M 318 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7732 (tm-30) REVERT: N 104 GLN cc_start: 0.8028 (pp30) cc_final: 0.7719 (pp30) REVERT: N 334 LYS cc_start: 0.8388 (pttt) cc_final: 0.8124 (pttm) REVERT: O 65 ASP cc_start: 0.8900 (m-30) cc_final: 0.8469 (p0) REVERT: O 137 LYS cc_start: 0.9276 (mmmt) cc_final: 0.9068 (mmmt) REVERT: P 1 MET cc_start: 0.6932 (tpp) cc_final: 0.6724 (tpp) REVERT: P 10 PHE cc_start: 0.8424 (p90) cc_final: 0.7992 (p90) REVERT: P 12 PHE cc_start: 0.8605 (m-80) cc_final: 0.8288 (m-80) REVERT: P 172 PHE cc_start: 0.8966 (m-80) cc_final: 0.8471 (m-80) REVERT: P 251 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7506 (tt) REVERT: A 36 LYS cc_start: 0.9042 (tptt) cc_final: 0.8592 (tptt) REVERT: A 107 LEU cc_start: 0.9420 (tp) cc_final: 0.9156 (pp) REVERT: A 138 TYR cc_start: 0.8547 (t80) cc_final: 0.8307 (t80) REVERT: A 140 LEU cc_start: 0.8732 (pp) cc_final: 0.8235 (mm) REVERT: A 177 MET cc_start: 0.6603 (mmt) cc_final: 0.6032 (mmp) REVERT: Q 2 SER cc_start: 0.5905 (m) cc_final: 0.5616 (p) REVERT: Q 27 ASN cc_start: 0.8986 (t0) cc_final: 0.8727 (t0) REVERT: Q 84 HIS cc_start: 0.8245 (p90) cc_final: 0.7997 (p90) REVERT: Q 115 MET cc_start: 0.8589 (mmp) cc_final: 0.8278 (mmt) REVERT: Q 121 LEU cc_start: 0.8309 (tp) cc_final: 0.8016 (tp) REVERT: Q 154 SER cc_start: 0.8477 (t) cc_final: 0.8235 (m) REVERT: Q 161 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8172 (tmmt) REVERT: Q 213 TYR cc_start: 0.6809 (t80) cc_final: 0.6442 (t80) outliers start: 85 outliers final: 73 residues processed: 478 average time/residue: 0.5193 time to fit residues: 415.4015 Evaluate side-chains 466 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 389 time to evaluate : 4.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 99 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 30 THR 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 148 ILE Chi-restraints excluded: chain K residue 38 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 334 LYS Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 88 PHE Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 242 LEU 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 193 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 275 ILE 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 51 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 ASP Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 261 PHE Chi-restraints excluded: chain N residue 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 325 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain P residue 20 TYR Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 136 TYR 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 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 344 GLN Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 497 PHE 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 169 optimal weight: 0.0980 chunk 15 optimal weight: 0.0470 chunk 368 optimal weight: 3.9990 chunk 404 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 337 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 333 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 overall best weight: 1.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 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** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN L 84 ASN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** M 59 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** ** Q 14 HIS ** 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 = 0.3871 r_free = 0.3871 target = 0.083802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.069698 restraints weight = 157796.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.071813 restraints weight = 90397.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.073264 restraints weight = 60267.029| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35031 Z= 0.152 Angle : 0.762 15.555 47821 Z= 0.372 Chirality : 0.048 0.344 5505 Planarity : 0.004 0.047 5856 Dihedral : 13.745 179.388 5545 Min Nonbonded Distance : 1.154 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.24 % Favored : 90.56 % Rotamer: Outliers : 2.01 % Allowed : 24.34 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 4144 helix: -0.79 (0.14), residues: 1346 sheet: -1.16 (0.21), residues: 604 loop : -2.25 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 58 HIS 0.010 0.002 HIS C 165 PHE 0.037 0.002 PHE A 56 TYR 0.033 0.002 TYR I 72 ARG 0.007 0.001 ARG Q 180 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 864) hydrogen bonds : angle 5.21084 ( 2380) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.58247 ( 12) covalent geometry : bond 0.00349 (35025) covalent geometry : angle 0.76234 (47809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13680.94 seconds wall clock time: 244 minutes 59.11 seconds (14699.11 seconds total)